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Pastor-López EJ, Escolà M, Kisielius V, Arias CA, Carvalho PN, Gorito AM, Ramos S, Freitas V, Guimarães L, Almeida CMR, Müller JA, Küster E, Kilian RM, Diawara A, Ba S, Matamoros V. Potential of nature-based solutions to reduce antibiotics, antimicrobial resistance, and pathogens in aquatic ecosystems. a critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174273. [PMID: 38925380 DOI: 10.1016/j.scitotenv.2024.174273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 06/03/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
This comprehensive scientific review evaluates the effectiveness of nature-based solutions (NBS) in reducing antibiotics (ABs), combating antimicrobial resistance (AMR), and controlling pathogens in various aquatic environments at different river catchment levels. It covers conventional and innovative treatment wetland configurations for wastewater treatment to reduce pollutant discharge into the aquatic ecosystems as well as exploring how river restoration and saltmarshes can enhance pollutant removal. Through the analysis of experimental studies and case examples, the review shows NBS's potential for providing sustainable and cost-effective solutions to improve the health of aquatic ecosystems. It also evaluates the use of diagnostic indicators to predict NBS effectiveness in removing specific pollutants such as ABs and AMR. The review concludes that NBS are feasible for addressing the new challenges stemming from human activities such as the presence of ABs, AMR and pathogens, contributing to a better understanding of NBS, highlighting success stories, addressing knowledge gaps, and providing recommendations for future research and implementation.
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Affiliation(s)
- Edward J Pastor-López
- Department of Environmental Chemistry, IDAEA-CSIC, c/Jordi Girona, 18-26, E-08034 Barcelona, Spain
| | - Mònica Escolà
- Department of Environmental Chemistry, IDAEA-CSIC, c/Jordi Girona, 18-26, E-08034 Barcelona, Spain
| | - Vaidotas Kisielius
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Carlos A Arias
- Department of Biology, Aarhus University, Aarhus, Denmark; WATEC - Centre for Water Technology, Aarhus University, Aarhus, Denmark
| | - Pedro N Carvalho
- Department of Environmental Science, Aarhus University, Roskilde, Denmark; WATEC - Centre for Water Technology, Aarhus University, Aarhus, Denmark
| | - Ana M Gorito
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal
| | - Sandra Ramos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal; Faculty of Sciences, University of Porto, Porto, Portugal
| | - Vânia Freitas
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal
| | - Laura Guimarães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal
| | - C Marisa R Almeida
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal; Faculty of Sciences, University of Porto, Porto, Portugal
| | - Jochen A Müller
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Eberhard Küster
- Helmholtz Centre for Environmental Research - UFZ, Dept. Bioanalytical Ecotoxicology, Leipzig, Germany
| | - R M Kilian
- Kilian Water Ltd., Torupvej 4, 8654 Bryrup, Denmark
| | - Abdoulaye Diawara
- Department of Geology and Mines, École Nationale d'Ingénieurs - Abderhamane Baba Touré (ENI-ABT), Bamako, Mali
| | - Sidy Ba
- Department of Geology and Mines, École Nationale d'Ingénieurs - Abderhamane Baba Touré (ENI-ABT), Bamako, Mali
| | - Víctor Matamoros
- Department of Environmental Chemistry, IDAEA-CSIC, c/Jordi Girona, 18-26, E-08034 Barcelona, Spain.
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2
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Zhao L, Guzman HP, Xagoraraki I. Tracking Chlamydia and Syphilis in the Detroit Metro Area by Molecular Analysis of Environmental Samples. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:17606-17616. [PMID: 39344309 DOI: 10.1021/acs.est.4c05869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
This paper describes one of the first studies applying wastewater surveillance to monitor Chlamydia and Syphilis and back-estimate infections in the community, based on bacterial shedding and wastewater surveillance data. Molecular biology laboratory methods were optimized, and a workflow was designed to implement wastewater surveillance tracking Chlamydia and Syphilis in the Detroit metro area (DMA), one of the most populous metropolitan areas in the U.S. Untreated composite wastewater samples were collected weekly from the three main interceptors that service DMA, which collect wastewater and discharge it to the Great Lakes Water Authority Water Resource Recovery Facility. Additionally, untreated wastewater was also collected from street manholes in three neighborhood sewersheds in Wayne, Macomb, and Oakland counties. Centrifugation, DNA extraction, and ddPCR methods were optimized and performed, targeting Chlamydia trachomatis and Treponema pallidum, the causative agents of Chlamydia and Syphilis, respectively. The limit of blank and limit of detection methods were determined experimentally for both targets. Both targets were detected and monitored in wastewater between December 25th, 2023, and April 22nd, 2024. The magnitudes of C. trachomatis and T. pallidum concentrations observed in neighborhood sewersheds were higher as compared to the concentrations observed in the interceptors. Infections of Chlamydia and Syphilis were back-estimated through an optimized formula based on shedding dynamics and wastewater surveillance data, which indicated potentially underreported conditions relative to publicly available clinical data.
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Affiliation(s)
- Liang Zhao
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct., East Lansing, Michigan 48823, United States
| | - Heidy Peidro Guzman
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct., East Lansing, Michigan 48823, United States
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct., East Lansing, Michigan 48823, United States
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3
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Tiwari A, Radu E, Kreuzinger N, Ahmed W, Pitkänen T. Key considerations for pathogen surveillance in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173862. [PMID: 38876348 DOI: 10.1016/j.scitotenv.2024.173862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024]
Abstract
Wastewater surveillance (WWS) has received significant attention as a rapid, sensitive, and cost-effective tool for monitoring various pathogens in a community. WWS is employed to assess the spatial and temporal trends of diseases and identify their early appearances and reappearances, as well as to detect novel and mutated variants. However, the shedding rates of pathogens vary significantly depending on factors such as disease severity, the physiology of affected individuals, and the characteristics of pathogen. Furthermore, pathogens may exhibit differential fate and decay kinetics in the sewerage system. Variable shedding rates and decay kinetics may affect the detection of pathogens in wastewater. This may influence the interpretation of results and the conclusions of WWS studies. When selecting a pathogen for WWS, it is essential to consider it's specific characteristics. If data are not readily available, factors such as fate, decay, and shedding rates should be assessed before conducting surveillance. Alternatively, these factors can be compared to those of similar pathogens for which such data are available.
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Affiliation(s)
- Ananda Tiwari
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Helsinki, Finland.
| | - Elena Radu
- Institute for Water Quality and Resource Management, Vienna University of Technology, Karlsplatz 13/226, 1040 Vienna, Austria; Stefan S. Nicolau Institute of Virology, Department of Cellular and Molecular Pathology, 285 Mihai Bravu Avenue, 030304 Bucharest, Romania; University of Medicine and Pharmacy Carol Davila, Department of Virology, 37 Dionisie Lupu Street, 020021 Bucharest, Romania.
| | - Norbert Kreuzinger
- Institute for Water Quality and Resource Management, Vienna University of Technology, Karlsplatz 13/226, 1040 Vienna, Austria.
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Helsinki, Finland.
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4
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Oliveira M, Antunes W, Mota S, Madureira-Carvalho Á, Dinis-Oliveira RJ, Dias da Silva D. An Overview of the Recent Advances in Antimicrobial Resistance. Microorganisms 2024; 12:1920. [PMID: 39338594 PMCID: PMC11434382 DOI: 10.3390/microorganisms12091920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 09/15/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
Antimicrobial resistance (AMR), frequently considered a major global public health threat, requires a comprehensive understanding of its emergence, mechanisms, advances, and implications. AMR's epidemiological landscape is characterized by its widespread prevalence and constantly evolving patterns, with multidrug-resistant organisms (MDROs) creating new challenges every day. The most common mechanisms underlying AMR (i.e., genetic mutations, horizontal gene transfer, and selective pressure) contribute to the emergence and dissemination of new resistant strains. Therefore, mitigation strategies (e.g., antibiotic stewardship programs-ASPs-and infection prevention and control strategies-IPCs) emphasize the importance of responsible antimicrobial use and surveillance. A One Health approach (i.e., the interconnectedness of human, animal, and environmental health) highlights the necessity for interdisciplinary collaboration and holistic strategies in combating AMR. Advancements in novel therapeutics (e.g., alternative antimicrobial agents and vaccines) offer promising avenues in addressing AMR challenges. Policy interventions at the international and national levels also promote ASPs aiming to regulate antimicrobial use. Despite all of the observed progress, AMR remains a pressing concern, demanding sustained efforts to address emerging threats and promote antimicrobial sustainability. Future research must prioritize innovative approaches and address the complex socioecological dynamics underlying AMR. This manuscript is a comprehensive resource for researchers, policymakers, and healthcare professionals seeking to navigate the complex AMR landscape and develop effective strategies for its mitigation.
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Affiliation(s)
- Manuela Oliveira
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, University Institute of Health Sciences—CESPU, Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal; (Á.M.-C.); (D.D.d.S.)
- UCIBIO—Research Unit on Applied Molecular Biosciences, Translational Toxicology Research Laboratory, University Institute of Health Sciences (1H-TOXRUN, IUCS-CESPU), Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal
| | - Wilson Antunes
- Instituto Universitário Militar, CINAMIL, Unidade Militar Laboratorial de Defesa Biológica e Química, Avenida Doutor Alfredo Bensaúde, 4 piso, do LNM, 1849-012 Lisbon, Portugal
| | - Salete Mota
- ULSEDV—Unidade Local De Saúde De Entre Douro Vouga, Unidade de Santa Maria da Feira e Hospital S. Sebastião, Rua Dr. Cândido Pinho, 4520-211 Santa Maria da Feira, Portugal
| | - Áurea Madureira-Carvalho
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, University Institute of Health Sciences—CESPU, Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal; (Á.M.-C.); (D.D.d.S.)
- UCIBIO—Applied Molecular Biosciences Unit, Forensics and Biomedical Sciences Research Laboratory, University Institute of Health Sciences (1H-TOXRUN, IUCS-CESPU), Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal
- Department of Public Health and Forensic Sciences and Medical Education, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Ricardo Jorge Dinis-Oliveira
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, University Institute of Health Sciences—CESPU, Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal; (Á.M.-C.); (D.D.d.S.)
- UCIBIO—Research Unit on Applied Molecular Biosciences, Translational Toxicology Research Laboratory, University Institute of Health Sciences (1H-TOXRUN, IUCS-CESPU), Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal
- Department of Public Health and Forensic Sciences and Medical Education, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
- FOREN—Forensic Science Experts, Avenida Dr. Mário Moutinho 33-A, 1400-136 Lisbon, Portugal
| | - Diana Dias da Silva
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, University Institute of Health Sciences—CESPU, Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal; (Á.M.-C.); (D.D.d.S.)
- UCIBIO—Applied Molecular Biosciences Unit, Forensics and Biomedical Sciences Research Laboratory, University Institute of Health Sciences (1H-TOXRUN, IUCS-CESPU), Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal
- REQUIMTE/LAQV, ESS, Polytechnic of Porto, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
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5
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Garner E, Maile-Moskowitz A, Angeles LF, Flach CF, Aga DS, Nambi I, Larsson DGJ, Bürgmann H, Zhang T, Vikesland PJ, Pruden A. Metagenomic Profiling of Internationally Sourced Sewage Influents and Effluents Yields Insight into Selecting Targets for Antibiotic Resistance Monitoring. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:16547-16559. [PMID: 39229966 PMCID: PMC11411718 DOI: 10.1021/acs.est.4c03726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
It has been debated whether wastewater treatment plants (WWTPs) primarily act to attenuate or amplify antibiotic resistance genes (ARGs). However, ARGs are highly diverse with respect to their resistance mechanisms, mobilities, and taxonomic hosts and therefore their behavior in WWTPs should not be expected to be universally conserved. We applied metagenomic sequencing to wastewater influent and effluent samples from 12 international WWTPs to classify the behavior of specific ARGs entering and exiting WWTPs. In total, 1079 different ARGs originating from a variety of bacteria were detected. This included ARGs that could be mapped to assembled scaffolds corresponding to nine human pathogens. While the relative abundance (per 16S rRNA gene) of ARGs decreased during treatment at 11 of the 12 WWTPs sampled and absolute abundance (per mL) decreased at all 12 WWTPs, increases in relative abundance were observed for 40% of the ARGs detected at the 12th WWTP. Also, the relative abundance of mobile genetic elements (MGE) increased during treatment, but the fraction of ARGs known to be transmissible between species decreased, thus demonstrating that increased MGE prevalence may not be generally indicative of an increase in ARGs. A distinct conserved resistome was documented in both influent and effluent across samples, suggesting that well-functioning WWTPs generally attenuate influent antibiotic resistance loads. This work helps inform strategies for wastewater surveillance of antibiotic resistance, highlighting the utility of tracking ARGs as indicators of treatment performance and relative risk reduction.
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Affiliation(s)
- Emily Garner
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Ayella Maile-Moskowitz
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Luisa F Angeles
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260, United States
| | - Carl-Fredrik Flach
- Institute of Biomedicine, Department of Infectious Diseases, Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Västra Götaland, SE-405 30 Gothenburg, Sweden
| | - Diana S Aga
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260, United States
| | - Indumathi Nambi
- Department of Civil Engineering, Indian Institute of Technology, Madras, Chennai 600036, India
| | - D G Joakim Larsson
- Institute of Biomedicine, Department of Infectious Diseases, Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Västra Götaland, SE-405 30 Gothenburg, Sweden
| | - Helmut Bürgmann
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum CH-6047, Switzerland
| | - Tong Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam 999077, Hong Kong
| | - Peter J Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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6
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Brauns B, Chandra S, Civil W, Lapworth DJ, MacDonald AM, McKenzie AA, Read DS, Sekhar M, Singer AC, Thankachan A, Tipper HJ. Presence of emerging organic contaminants and microbial indicators in surface water and groundwater in urban India. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024:124983. [PMID: 39293652 DOI: 10.1016/j.envpol.2024.124983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 08/02/2024] [Accepted: 09/15/2024] [Indexed: 09/20/2024]
Abstract
This study presents a first combined assessment of emerging organic contaminants (EOC) and antimicrobial resistance (AMR) indicators in the South Indian city of Bengaluru from multiple sources, addressing a knowledge gap on EOCs and AMR occurrences and relationships in different water sources in urban India. A unique approach in this study was to combine the detection of EOCs with an assessment of the AMR-indicating class 1 integron-integrase gene, intI1. Twenty-five samples collected from groundwater, local surface waters, and tap water imported from the Cauvery Basin were screened for 1499 EOCs. A total of 125 EOCs were detected at concentrations per compound of up to 314 μg/L. Concentrations for a range of contaminants were higher than those previously detected in Indian groundwaters. High concentrations of Per- and polyfluoroalkyl substances (PFAS) were detected with up to 1.8 μg/L in surface water and up to 0.9 μg/L in groundwater. Calculated risk quotients indicated potential AMR development caused by high concentrations of azithromycin, fluconazole, and sulfanilamide in surface waters that have little protection against sewage inflows. Surface waters that have recently undergone environmental restoration (e.g., removing silted bottom layers and enhancing protection against encroachments and sewage inflows) had lower EOC detections and risk of AMR development. Specific EOC detections, e.g., the ubiquitous detection of the sweetener sucralose (in use since ∼2000), indicated recent groundwater recharge and a contribution of imported Cauvery River water for recharge. This study highlights the need for monitoring and water protection, the role of EOCs as potential drivers of AMR, and the success of surface water protection measures to improve freshwater quality.
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Affiliation(s)
- Bentje Brauns
- British Geological Survey (BGS), Environmental Science Centre, Keyworth, Nottingham, NG12 5GG, UK
| | - Subhash Chandra
- Department of Mines and Geology, Government of Karnataka, Karnataka 562159, India
| | - Wayne Civil
- National Laboratory Service, Starcross, Exeter, EX6 8DF, UK
| | - Dan J Lapworth
- British Geological Survey (BGS), Maclean Building, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Alan M MacDonald
- British Geological Survey (BGS), The Lyell Centre, Edinburgh EH14 4AP, UK
| | - Andrew A McKenzie
- British Geological Survey (BGS), Maclean Building, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Daniel S Read
- UK Centre of Ecology and Hydrology (UKCEH), Maclean Building, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Muddu Sekhar
- Department of Civil Engineering, Indian Institute of Science (IISc), Bengaluru, Karnataka 560012, India
| | - Andrew C Singer
- UK Centre of Ecology and Hydrology (UKCEH), Maclean Building, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Amritha Thankachan
- University of Visvesvaraya College of Engineering, Bangalore University, Bengaluru, Karnataka 560001, India
| | - Holly J Tipper
- UK Centre of Ecology and Hydrology (UKCEH), Maclean Building, Crowmarsh Gifford, Wallingford OX10 8BB, UK
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7
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Jiang P, Sun S, Goh SG, Tong X, Chen Y, Yu K, He Y, Gin KYH. A rapid approach with machine learning for quantifying the relative burden of antimicrobial resistance in natural aquatic environments. WATER RESEARCH 2024; 262:122079. [PMID: 39047454 DOI: 10.1016/j.watres.2024.122079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 06/05/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024]
Abstract
The massive use and discharge of antibiotics have led to increasing concerns about antimicrobial resistance (AMR) in natural aquatic environments. Since the dose-response mechanisms of pathogens with AMR have not yet been fully understood, and the antibiotic resistance genes and bacteria-related data collection via field sampling and laboratory testing is time-consuming and expensive, designing a rapid approach to quantify the burden of AMR in the natural aquatic environment has become a challenge. To cope with such a challenge, a new approach involving an integrated machine-learning framework was developed by investigating the associations between the relative burden of AMR and easily accessible variables (i.e., relevant environmental variables and adjacent land-use patterns). The results, based on a real-world case analysis, demonstrate that the quantification speed has been reduced from 3-7 days, which is typical for traditional measurement procedures with field sampling and laboratory testing, to approximately 0.5 hours using the new approach. Moreover, all five metrics for AMR relative burden quantification exceed the threshold level of 85%, with F1-score surpassing 0.92. Compared to logistic regression, decision trees, and basic random forest, the adaptive random forest model within the framework significantly improves quantification accuracy without sacrificing model interpretability. Two environmental variables, dissolved oxygen and resistivity, along with the proportion of green areas were identified as three key feature variables for the rapid quantification. This study contributes to the enrichment of burden analyses and management practices for rapid quantification of the relative burden of AMR without dose-response information.
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Affiliation(s)
- Peng Jiang
- Department of Industrial Engineering and Management, Business School, Sichuan University, Chengdu 610064, China; NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore.
| | - Shuyi Sun
- Department of Industrial Engineering and Management, Business School, Sichuan University, Chengdu 610064, China; Department of Industrial Systems Engineering & Management, National University of Singapore, Singapore 119260, Singapore
| | - Shin Giek Goh
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Xuneng Tong
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Yihan Chen
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Kaifeng Yu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore; Department of Civil & Environmental Engineering, National University of Singapore, Singapore 117576, Singapore.
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8
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Kawabe H, Manfio L, Pena SM, Zhou NA, Bradley KM, Chen C, McLendon C, Benner SA, Levy K, Yang Z, Marchand JA, Fuhrmeister ER. Harnessing non-standard nucleic acids for highly sensitive icosaplex (20-plex) detection of microbial threats. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.09.24313328. [PMID: 39314929 PMCID: PMC11419210 DOI: 10.1101/2024.09.09.24313328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Environmental surveillance and clinical diagnostics heavily rely on the polymerase chain reaction (PCR) for target detection. A growing list of microbial threats warrants new PCR-based detection methods that are highly sensitive, specific, and multiplexable. Here, we introduce a PCR-based icosaplex (20-plex) assay for detecting 18 enteropathogen and two antimicrobial resistance genes. This multiplexed PCR assay leverages the self-avoiding molecular recognition system (SAMRS) to avoid primer dimer formation, the artificially expanded genetic information system (AEGIS) for amplification specificity, and next-generation sequencing for amplicon identification. We benchmarked this assay using a low-cost, portable sequencing platform (Oxford Nanopore) on wastewater, soil, and human stool samples. Using parallelized multi-target TaqMan Array Cards (TAC) to benchmark performance of the 20-plex assay, there was 74% agreement on positive calls and 97% agreement on negative calls. Additionally, we show how sequencing information from the 20-plex can be used to further classify allelic variants of genes and distinguish sub-species. The strategy presented offers sensitive, affordable, and robust multiplex detection that can be used to support efforts in wastewater-based epidemiology, environmental monitoring, and human/animal diagnostics.
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Affiliation(s)
- Hinako Kawabe
- Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Luran Manfio
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
| | - Sebastian Magana Pena
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
| | - Nicolette A. Zhou
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Seattle, WA, 98195, USA
| | - Kevin M. Bradley
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Cen Chen
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Chris McLendon
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Karen Levy
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Seattle, WA, 98195, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Jorge A. Marchand
- Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
- Molecular Engineering and Science Institute, University of Washington, Seattle, Seattle, WA, 98195, USA
| | - Erica R. Fuhrmeister
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Seattle, WA, 98195, USA
- Civil and Environmental Engineering, University of Washington, Seattle, Seattle, WA, 98195, USA
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9
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Mourkas E, Valdebenito JO, Marsh H, Hitchings MD, Cooper KK, Parker CT, Székely T, Johansson H, Ellström P, Pascoe B, Waldenström J, Sheppard SK. Proximity to humans is associated with antimicrobial-resistant enteric pathogens in wild bird microbiomes. Curr Biol 2024; 34:3955-3965.e4. [PMID: 39142288 DOI: 10.1016/j.cub.2024.07.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/21/2024] [Accepted: 07/16/2024] [Indexed: 08/16/2024]
Abstract
Humans are radically altering global ecology, and one of the most apparent human-induced effects is urbanization, where high-density human habitats disrupt long-established ecotones. Changes to these transitional areas between organisms, especially enhanced contact among humans and wild animals, provide new opportunities for the spread of zoonotic pathogens. This poses a serious threat to global public health, but little is known about how habitat disruption impacts cross-species pathogen spread. Here, we investigated variation in the zoonotic enteric pathogen Campylobacter jejuni. The ubiquity of C. jejuni in wild bird gut microbiomes makes it an ideal organism for understanding how host behavior and ecology influence pathogen transition and spread. We analyzed 700 C. jejuni isolate genomes from 30 bird species in eight countries using a scalable generalized linear model approach. Comparing multiple behavioral and ecological traits showed that proximity to human habitation promotes lineage diversity and is associated with antimicrobial-resistant (AMR) strains in natural populations. Specifically, wild birds from urban areas harbored up to three times more C. jejuni genotypes and AMR genes. This study provides novel methodology and much-needed quantitative evidence linking urbanization to gene pool spread and zoonoses.
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Affiliation(s)
- Evangelos Mourkas
- Ineos Oxford Institute, Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Zoonosis Science Centre, Department of Medical Sciences, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - José O Valdebenito
- Bird Ecology Lab, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Independencia 631, 5110566 Valdivia, Chile; Centro de Humedales Río Cruces (CEHUM), Universidad Austral de Chile, Camino Cabo Blanco Alto s/n, 5090000 Valdivia, Chile; HUN-REN-DE Reproductive Strategies Research Group, Department of Evolutionary Zoology and Human Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, 8320000 Santiago, Chile
| | - Hannah Marsh
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Matthew D Hitchings
- Institute of Life Science, Swansea University Medical School, Swansea University, Singleton Park, SA2 8PP Swansea, Wales
| | - Kerry K Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, 1117 E. Lowell St., Tucson, AZ 85721, USA
| | - Craig T Parker
- Produce Safety and Microbiology Unit, Western Region Research Center, USDA, Agricultural Research Service, Albany, CA 94710, USA
| | - Tamás Székely
- HUN-REN-DE Reproductive Strategies Research Group, Department of Evolutionary Zoology and Human Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Håkan Johansson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Stuvaregatan 2, 392 31 Kalmar, Sweden
| | - Patrik Ellström
- Zoonosis Science Centre, Department of Medical Sciences, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Ben Pascoe
- Ineos Oxford Institute, Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Stuvaregatan 2, 392 31 Kalmar, Sweden
| | - Samuel K Sheppard
- Ineos Oxford Institute, Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
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10
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Kotzamanidis C, Malousi A, Paraskeva A, Vafeas G, Giantzi V, Hatzigiannakis E, Dalampakis P, Kinigopoulou V, Vrouhakis I, Zouboulis A, Yiangou M, Zdragas A. River waters in Greece: A reservoir for clinically relevant extended-spectrum-β-lactamases-producing Escherichia coli. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 941:173554. [PMID: 38823724 DOI: 10.1016/j.scitotenv.2024.173554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/10/2024] [Accepted: 05/24/2024] [Indexed: 06/03/2024]
Abstract
In the current study, the genotypic characteristics such as antimicrobial resistance and virulence genes, and plasmid replicons and phenotypic characteristics such as biofilm formation and antimicrobial resistance of 87 extended-spectrum beta-lactamase (ESBL)-producing E. coli (ESBL-Ec) isolated from 7 water bodies in northern Greece were investigated. Our data show a high prevalence (60.0 %) of ESBL-Ec in surface waters that exhibit high genetic diversity, suggesting multiple sources of their transmission into the aquatic environment. When evaluating the antimicrobial resistance of isolates, wide variation in their resistance profiles has been detected, with all isolates being multi-drug resistant (MDR). Regarding biofilm formation capacity and phylogenetic groups, the majority (54.0 %, 47/87) of ESBL-Ec were classified as no biofilm producers mainly assigned to phylogroup A (35.6 %; 31/87), followed by B2 (26.5 %; 23/87). PCR screening showed that a high proportion of the isolates tested positive for the blaCTX-M-1 group genes (69 %, 60/87), followed by blaTEM (55.2 %, 48/87), blaOXA (25.3 %, 22/87) and blaCTX-M-9 (17.2 %, 15/87). A subset of 28 ESBL-Ec strains was further investigated by applying whole genome sequencing (WGS), and among them, certain clinically significant sequence types were identified, such as ST131 and ST10. The corresponding in silico analysis predicted all these isolates as human pathogens, while a significant proportion of WGS-ESBL-Ec were assigned to extraintestinal pathogenic E. coli (ExPEC; 32.1 %), and urinary pathogenic E. coli (UPEC; 28.6 %) pathotypes. Comparative phylogenetic analysis, showed that the genomes of the ST131-O25:H4-H30 isolates are genetically linked to the human clinical strains. Here, we report for the first time the detection of a plasmid-mediated mobile colistin resistance gene in ESBL-Ec in Greece isolated from an environmental source. Overall, this study underlines the role of surface waters as a reservoir for antibiotic resistance genes and for presumptive pathogenic ESBL-Ec.
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Affiliation(s)
- Charalampos Kotzamanidis
- Veterinary Research Institute of Thessaloniki, Hellenic Agricultural Organisation-DEMETER, Campus of Thermi, Thermi 570 01, Greece.
| | - Andigoni Malousi
- School of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece; Genomics and Epigenomics Translational Research Group, Center for Interdisciplinary Research and Innovation, Thessaloniki 57001, Greece
| | - Anastasia Paraskeva
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - George Vafeas
- Veterinary Research Institute of Thessaloniki, Hellenic Agricultural Organisation-DEMETER, Campus of Thermi, Thermi 570 01, Greece
| | - Virginia Giantzi
- Veterinary Research Institute of Thessaloniki, Hellenic Agricultural Organisation-DEMETER, Campus of Thermi, Thermi 570 01, Greece
| | - Evaggelos Hatzigiannakis
- Soil & Water Resources Institute, Hellenic Agricultural Organisation-DEMETER, Sindos, Central Macedonia 57400, Greece
| | - Paschalis Dalampakis
- Soil & Water Resources Institute, Hellenic Agricultural Organisation-DEMETER, Sindos, Central Macedonia 57400, Greece
| | - Vasiliki Kinigopoulou
- Soil & Water Resources Institute, Hellenic Agricultural Organisation-DEMETER, Sindos, Central Macedonia 57400, Greece
| | - Ioannis Vrouhakis
- Soil & Water Resources Institute, Hellenic Agricultural Organisation-DEMETER, Sindos, Central Macedonia 57400, Greece
| | - Anastasios Zouboulis
- Department of Chemistry, Division of Chemical & Industrial Technology, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Minas Yiangou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Antonios Zdragas
- Veterinary Research Institute of Thessaloniki, Hellenic Agricultural Organisation-DEMETER, Campus of Thermi, Thermi 570 01, Greece
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11
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Ma L, Lyu W, Zeng T, Wang W, Chen Q, Zhao J, Zhang G, Lu L, Yang H, Xiao Y. Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition. IMETA 2024; 3:e198. [PMID: 39135685 PMCID: PMC11316934 DOI: 10.1002/imt2.198] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/18/2024] [Accepted: 04/20/2024] [Indexed: 08/15/2024]
Abstract
The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play an important role in duck health and production. Here, we constructed the first relatively comprehensive duck gut microbial gene catalog (24 million genes) and 4437 metagenome-assembled genomes using 375 GIT metagenomic samples from four different duck breeds across five intestinal segments under two distinct rearing conditions. We further characterized the intestinal region-specific microbial taxonomy and their assigned functions, as well as the temporal development and maturation of the duck gut microbiome. Our metagenomic analysis revealed the similarity within the microbiota of the foregut and hindgut compartments, but distinctive taxonomic and functional differences between distinct intestinal segments. In addition, we found a significant shift in the microbiota composition of newly hatched ducks (3 days), followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days), indicating that the intestinal microbiota develops into a relatively mature and stable community as the host duck matures. Comparing the impact of different rearing conditions (with and without water) on duck cecal microbiota communities and functions, we found that the bacterial capacity for lipopolysaccharide biosynthesis was significantly increased in ducks that had free access to water, leading to the accumulation of pathogenic bacteria and antibiotic-resistance genes. Taken together, our findings expand the understanding of the microbiome signatures linked to intestinal regional, temporal development, and rearing conditions in ducks, which highlight the significant impact of microbiota on poultry health and production.
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Affiliation(s)
- Lingyan Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Agro‐product Safety and NutritionZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Wentao Lyu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Agro‐product Safety and NutritionZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Tao Zeng
- Institute of Animal Husbandry and Veterinary MedicineZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Wen Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Agro‐product Safety and NutritionZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Qu Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Agro‐product Safety and NutritionZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Jiangchao Zhao
- Department of Animal Science, Division of AgricultureUniversity of ArkansasFayettevilleArkansasUSA
| | - Guolong Zhang
- Department of Animal and Food SciencesOklahoma State UniversityStillwaterOklahomaUSA
| | - Lizhi Lu
- Institute of Animal Husbandry and Veterinary MedicineZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Agro‐product Safety and NutritionZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Yingping Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Agro‐product Safety and NutritionZhejiang Academy of Agricultural SciencesHangzhouChina
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12
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Riffat I, Shah A. Electrochemical and optical protocols for the detection and removal of an antibiotic drug rifaximin from wastewater. RSC Adv 2024; 14:22867-22876. [PMID: 39035716 PMCID: PMC11259106 DOI: 10.1039/d4ra04309j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024] Open
Abstract
Improper disposal of pharmaceutical drugs is increasing the pollution level of water reservoirs which in turn adversely impacts the ecosystem. The current study presents an electrochemical scaffold that comprises a glassy carbon electrode modified with amino-functionalized multiwalled carbon nanotubes (NH2-fMWCNTs) for the detection of a pharmaceutical drug rifaximin in wastewater. Electrochemical impedance spectroscopic characterization revealed efficient charge transport through the modified electrode surface. Square wave voltammetry was employed for probing the electro-oxidation of antibiotic rifaximin. Under optimized experimental conditions, the designed sensor demonstrated the qualities of sensitivity, repeatability, and reproducibility as required for the practical applicability of the sensing device. After the detection of a contaminant, its removal from water is imperative. In this regard an adsorption method using ZnO nanoparticles as adsorbents was developed that led to the removal of rifaximin from wastewater. At lower adsorbate concentration, adsorption was found to occur according to the Langmuir model while at higher concentration adsorption data followed the Freundlich model. The rate of rifaximin adsorption over ZnO nanoparticles followed pseudo-second-order kinetics.
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Affiliation(s)
- Ifra Riffat
- Department of Chemistry, Quaid-i-Azam University Islamabad 45320 Pakistan
| | - Afzal Shah
- Department of Chemistry, Quaid-i-Azam University Islamabad 45320 Pakistan
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13
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Wang F, Xiang L, Sze-Yin Leung K, Elsner M, Zhang Y, Guo Y, Pan B, Sun H, An T, Ying G, Brooks BW, Hou D, Helbling DE, Sun J, Qiu H, Vogel TM, Zhang W, Gao Y, Simpson MJ, Luo Y, Chang SX, Su G, Wong BM, Fu TM, Zhu D, Jobst KJ, Ge C, Coulon F, Harindintwali JD, Zeng X, Wang H, Fu Y, Wei Z, Lohmann R, Chen C, Song Y, Sanchez-Cid C, Wang Y, El-Naggar A, Yao Y, Huang Y, Cheuk-Fung Law J, Gu C, Shen H, Gao Y, Qin C, Li H, Zhang T, Corcoll N, Liu M, Alessi DS, Li H, Brandt KK, Pico Y, Gu C, Guo J, Su J, Corvini P, Ye M, Rocha-Santos T, He H, Yang Y, Tong M, Zhang W, Suanon F, Brahushi F, Wang Z, Hashsham SA, Virta M, Yuan Q, Jiang G, Tremblay LA, Bu Q, Wu J, Peijnenburg W, Topp E, Cao X, Jiang X, Zheng M, Zhang T, Luo Y, Zhu L, Li X, Barceló D, Chen J, Xing B, Amelung W, Cai Z, Naidu R, Shen Q, Pawliszyn J, Zhu YG, Schaeffer A, Rillig MC, Wu F, Yu G, Tiedje JM. Emerging contaminants: A One Health perspective. Innovation (N Y) 2024; 5:100612. [PMID: 38756954 PMCID: PMC11096751 DOI: 10.1016/j.xinn.2024.100612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/10/2024] [Indexed: 05/18/2024] Open
Abstract
Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leilei Xiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kelvin Sze-Yin Leung
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
- HKBU Institute of Research and Continuing Education, Shenzhen Virtual University Park, Shenzhen, China
| | - Martin Elsner
- Technical University of Munich, TUM School of Natural Sciences, Institute of Hydrochemistry, 85748 Garching, Germany
| | - Ying Zhang
- School of Resources & Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yuming Guo
- Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Bo Pan
- Faculty of Environmental Science & Engineering, Kunming University of Science & Technology, Kunming 650500, China
| | - Hongwen Sun
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Taicheng An
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Guangguo Ying
- Ministry of Education Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou, Guangdong 510006, China
| | - Bryan W. Brooks
- Department of Environmental Science, Baylor University, Waco, TX, USA
- Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University, Waco, TX, USA
| | - Deyi Hou
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Damian E. Helbling
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Jianqiang Sun
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hao Qiu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Timothy M. Vogel
- Laboratoire d’Ecologie Microbienne, Universite Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622 Villeurbanne, France
| | - Wei Zhang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang Road 1, Nanjing 210095, China
| | - Myrna J. Simpson
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Yi Luo
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Scott X. Chang
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, AB T6G 2E3, Canada
| | - Guanyong Su
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Bryan M. Wong
- Materials Science & Engineering Program, Department of Chemistry, and Department of Physics & Astronomy, University of California-Riverside, Riverside, CA, USA
| | - Tzung-May Fu
- Shenzhen Key Laboratory of Precision Measurement and Early Warning Technology for Urban Environmental Health Risks, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Karl J. Jobst
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Avenue, St. John’s, NL A1C 5S7, Canada
| | - Chengjun Ge
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Ecological and Environmental Sciences, Hainan University, Haikou 570228, China
| | - Frederic Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Jean Damascene Harindintwali
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiankui Zeng
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Haijun Wang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Yuhao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Rainer Lohmann
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Changer Chen
- Ministry of Education Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou, Guangdong 510006, China
| | - Yang Song
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Concepcion Sanchez-Cid
- Environmental Microbial Genomics, UMR 5005 Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, Écully, France
| | - Yu Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ali El-Naggar
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, AB T6G 2E3, Canada
- Department of Soil Sciences, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Yiming Yao
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yanran Huang
- Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong, China
| | | | - Chenggang Gu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huizhong Shen
- Shenzhen Key Laboratory of Precision Measurement and Early Warning Technology for Urban Environmental Health Risks, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yanpeng Gao
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang Road 1, Nanjing 210095, China
| | - Hao Li
- Faculty of Environmental Science & Engineering, Kunming University of Science & Technology, Kunming 650500, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Natàlia Corcoll
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Min Liu
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Daniel S. Alessi
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB T6G 2E3, Canada
| | - Hui Li
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Kristian K. Brandt
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Sino-Danish Center (SDC), Beijing, China
| | - Yolanda Pico
- Food and Environmental Safety Research Group of the University of Valencia (SAMA-UV), Desertification Research Centre - CIDE (CSIC-UV-GV), Road CV-315 km 10.7, 46113 Moncada, Valencia, Spain
| | - Cheng Gu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jianqiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Philippe Corvini
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, 4132 Muttenz, Switzerland
| | - Mao Ye
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Teresa Rocha-Santos
- Centre for Environmental and Marine Studies (CESAM) & Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Huan He
- Jiangsu Engineering Laboratory of Water and Soil Eco-remediation, School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Meiping Tong
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Weina Zhang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Fidèle Suanon
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Laboratory of Physical Chemistry, Materials and Molecular Modeling (LCP3M), University of Abomey-Calavi, Republic of Benin, Cotonou 01 BP 526, Benin
| | - Ferdi Brahushi
- Department of Environment and Natural Resources, Agricultural University of Tirana, 1029 Tirana, Albania
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, and School of Environment & Ecology, Jiangnan University, Wuxi 214122, China
| | - Syed A. Hashsham
- Center for Microbial Ecology, Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Marko Virta
- Department of Microbiology, University of Helsinki, 00010 Helsinki, Finland
| | - Qingbin Yuan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Gaofei Jiang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Louis A. Tremblay
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa 1142, New Zealand
| | - Qingwei Bu
- School of Chemical & Environmental Engineering, China University of Mining & Technology - Beijing, Beijing 100083, China
| | - Jichun Wu
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Willie Peijnenburg
- National Institute of Public Health and the Environment, Center for the Safety of Substances and Products, 3720 BA Bilthoven, The Netherlands
- Leiden University, Center for Environmental Studies, Leiden, the Netherlands
| | - Edward Topp
- Agroecology Mixed Research Unit, INRAE, 17 rue Sully, 21065 Dijon Cedex, France
| | - Xinde Cao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minghui Zheng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Taolin Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongming Luo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiangdong Li
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Damià Barceló
- Chemistry and Physics Department, University of Almeria, 04120 Almeria, Spain
| | - Jianmin Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, USA
| | - Wulf Amelung
- Institute of Crop Science and Resource Conservation (INRES), Soil Science and Soil Ecology, University of Bonn, 53115 Bonn, Germany
- Agrosphere Institute (IBG-3), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Ravi Naidu
- Global Centre for Environmental Remediation (GCER), The University of Newcastle (UON), Newcastle, NSW 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), The University of Newcastle (UON), Newcastle, NSW 2308, Australia
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Yong-guan Zhu
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Andreas Schaeffer
- Institute for Environmental Research, RWTH Aachen University, 52074 Aachen, Germany
| | - Matthias C. Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Gang Yu
- Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhuhai, China
| | - James M. Tiedje
- Center for Microbial Ecology, Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
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14
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Symochko L, Pereira P, Demyanyuk O, Pinheiro MC, Barcelo D. Resistome in a changing environment: Hotspots and vectors of spreading with a focus on the Russian-Ukrainian War. Heliyon 2024; 10:e32716. [PMID: 39183836 PMCID: PMC11341293 DOI: 10.1016/j.heliyon.2024.e32716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/22/2024] [Accepted: 06/07/2024] [Indexed: 08/27/2024] Open
Abstract
This work aims to shed light on the key factors contributing to the development of environmental resistance and the urgent need to address the growing problem of antibiotic resistance (AR) under the Russian-Ukrainian conflict. The article provides an overview of the main mechanisms involved in AR development and dissemination globally and the challenges posed by the ongoing war in Ukraine. The work outlines various international initiatives to reduce AR, including the concept of "One Health" and the strategies established, which are the key to reducing the effects on public health. Addressing AR globally and in conflict areas requires a comprehensive approach. This involves implementing monitoring of the microorganism's resistance levels to antibiotics, controlling the use of antimicrobial drugs, increasing public awareness of the AR, introducing educational programs to prevent the improper use of antibiotics, and adopting environmentally safe methods for the disposal of waste from medical, food, and other industries that produce or use antibiotics. Such initiatives are essential for promoting the responsible use of antibiotics, preventing the spread of AR infections, and preserving the effectiveness of existing antimicrobial drugs.
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Affiliation(s)
- L. Symochko
- Uzhhorod National University, Uzhhorod, Ukraine
- University of Coimbra, Coimbra, Portugal
- Institute of Agroecology and Environmental Management NAAS, Kyiv, Ukraine
| | - P. Pereira
- Environmental Management Laboratory, Mykolas Romeris University, Vilnius, Lithuania
| | - O. Demyanyuk
- Institute of Agroecology and Environmental Management NAAS, Kyiv, Ukraine
| | - M.N. Coelho Pinheiro
- Polytechnic Institute of Coimbra, Coimbra Institute of Engineering, Coimbra, Portugal
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15
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Donchev D, Ivanov IN, Stoikov I, Ivanova M. Metagenomic Investigation of the Short-Term Temporal and Spatial Dynamics of the Bacterial Microbiome and the Resistome Downstream of a Wastewater Treatment Plant in the Iskar River in Bulgaria. Microorganisms 2024; 12:1250. [PMID: 38930632 PMCID: PMC11207046 DOI: 10.3390/microorganisms12061250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/14/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Waste Water Treatment Plants (WWTP) aim to reduce contamination in effluent water; however, studies indicate antimicrobial resistance genes (ARGs) persist post-treatment, potentially leading to their spread from human populated areas into the environment. This study evaluated the impact of a large WWTP serving 125,000 people on the Iskar River in Bulgaria, by characterizing the spatial and short-term temporal dynamics in bacterial community dynamics and resistance profiles of the surface water. Pairs of samples were collected biweekly on four dates from two different locations, one about 800 m after the WWTP effluents and the other 10 km downstream. Taxonomic classification revealed the dominance of Pseudomonodota and Bacteriodota, notably the genera Flavobacterium, Aquirufa, Acidovorax, Polynucleobacter, and Limnohabitans. The taxonomic structure corresponded with both lentic and lotic freshwater habitats, with Flavobacterium exhibiting a significant decrease over the study period. Principal Coordinate Analysis revealed statistically significant differences in bacterial community composition between samples collected on different dates. Differential abundance analysis identified notable enrichment of Polynucleobacter and Limnohabitans. There were shifts within the enriched or depleted bacterial taxa between early and late sampling dates. High relative abundance of the genes erm(B), erm(F), mph(E), msr(E) (macrolides); tet(C), tet(O), tet(W), tet(Q) and tet(X) (tetracyclines); sul1 and sul2 (sulphonamides); and cfxA3, cfxA6 (beta-lactams) were detected, with trends of increased presence in the latest sampling dates and in the location closer to the WWTP. Of note, genes conferring resistance to carbapenems blaOXA-58 and blaIMP-33-like were identified. Co-occurrence analysis of ARGs and mobile genetic elements on putative plasmids showed few instances, and the estimated human health risk score (0.19) according to MetaCompare2.0 was low. In total, 29 metagenome-assembled genomes were recovered, with only a few harbouring ARGs. This study enhances our understanding of freshwater microbial community dynamics and antibiotic resistance profiles, highlighting the need for continued ARGs monitoring.
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Affiliation(s)
- Deyan Donchev
- National Reference Laboratory for Control and Monitoring of Antimicrobial Resistance, Department of Microbiology, National Center of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Ivan N. Ivanov
- National Reference Laboratory for Control and Monitoring of Antimicrobial Resistance, Department of Microbiology, National Center of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Ivan Stoikov
- National Reference Laboratory for Control and Monitoring of Antimicrobial Resistance, Department of Microbiology, National Center of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Monika Ivanova
- Paralax Life Sciences, Sofia Center, 47 Bacho Kiro Str., 1202 Sofia, Bulgaria
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16
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Flores-Vargas G, Bergsveinson J, Korber DR. Environmentally Relevant Antibiotic Concentrations Exert Stronger Selection Pressure on River Biofilm Resistomes than AMR-Reservoir Effluents. Antibiotics (Basel) 2024; 13:539. [PMID: 38927205 PMCID: PMC11200958 DOI: 10.3390/antibiotics13060539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Freshwater environments are primary receiving systems of wastewater and effluents, which carry low concentrations of antibiotics and antimicrobial-resistant (AMR) bacteria and genes. Aquatic microbial communities are thus exposed to environmentally relevant concentrations of antibiotics (ERCA) that presumably influence the acquisition and spread of environmental AMR. Here, we analyzed ERCA exposure with and without the additional presence of municipal wastewater treatment plant effluent (W) and swine manure run-off (M) on aquatic biofilm resistomes. Microscopic analyses revealed decreased taxonomic diversity and biofilm structural integrity, while metagenomic analysis revealed an increased abundance of resistance, virulence, and mobile element-related genes at the highest ERCA exposure levels, with less notable impacts observed when solely exposed to W or M effluents. Microbial function predictions indicated increased gene abundance associated with energy and cell membrane metabolism and heavy metal resistance under ERCA conditions. In silico predictions of increased resistance mechanisms did not correlate with observed phenotypic resistance patterns when whole communities were exposed to antimicrobial susceptibility testing. This reveals important insight into the complexity of whole-community coordination of physical and genetic responses to selective pressures. Lastly, the environmental AMR risk assessment of metagenomic data revealed a higher risk score for biofilms grown at sub-MIC antibiotic conditions.
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Affiliation(s)
- Gabriela Flores-Vargas
- Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada;
| | - Jordyn Bergsveinson
- Environment and Climate Change Canada, 11 Innovation Blvd., Saskatoon, SK S7N 3H5, Canada;
| | - Darren R. Korber
- Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada;
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17
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McConn BR, Kraft AL, Durso LM, Ibekwe AM, Frye JG, Wells JE, Tobey EM, Ritchie S, Williams CF, Cook KL, Sharma M. An analysis of culture-based methods used for the detection and isolation of Salmonella spp., Escherichia coli, and Enterococcus spp. from surface water: A systematic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172190. [PMID: 38575025 DOI: 10.1016/j.scitotenv.2024.172190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/14/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Identification of methods for the standardized assessment of bacterial pathogens and antimicrobial resistance (AMR) in environmental water can improve the quality of monitoring and data collected, support global surveillance efforts, and enhance the understanding of environmental water sources. We conducted a systematic review to assemble and synthesize available literature that identified methods for assessment of prevalence and abundance of bacterial fecal indicators and pathogens in water for the purposes of monitoring bacterial pathogens and AMR. After screening for quality, 175 unique publications were identified from 15 databases, and data were extracted for analysis. This review identifies the most common and robust methods, and media used to isolate target organisms from surface water sources, summarizes methodological trends, and recognizes knowledge gaps. The information presented in this review will be useful when establishing standardized methods for monitoring bacterial pathogens and AMR in water in the United States and globally.
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Affiliation(s)
- Betty R McConn
- Oak Ridge Institute of Science and Education/U.S. Department of Agriculture (USDA), Agricultural Research Service, Beltsville, MD, United States of America
| | - Autumn L Kraft
- Oak Ridge Institute of Science and Education/U.S. Department of Agriculture (USDA), Agricultural Research Service, Beltsville, MD, United States of America
| | - Lisa M Durso
- USDA ARS Agroecoystem Management Research, Lincoln, NE, United States of America
| | - Abasiofiok M Ibekwe
- USDA ARS, Agricultural Water Efficiency and Salinity Research Unit, Riverside, CA, United States of America
| | - Jonathan G Frye
- USDA ARS, U.S. National Poultry Research Center, Poultry Microbiological Safety and Processing Research Unit, Athens, GA, United States of America
| | - James E Wells
- USDA ARS, U.S. Meat Animal Research Center, Meat Safety and Quality, Clay Center, NE, United States of America
| | - Elizabeth M Tobey
- USDA National Agricultural Library, Beltsville, MD, United States of America
| | - Stephanie Ritchie
- USDA National Agricultural Library, Beltsville, MD, United States of America
| | - Clinton F Williams
- USDA ARS, US Arid-Land Agricultural Research Center, Maricopa, AZ, United States of America
| | - Kimberly L Cook
- USDA ARS, Nutrition, Food Safety and Quality National Program Staff, Beltsville, MD, United States of America
| | - Manan Sharma
- USDA ARS Environmental Microbial and Food Safety Laboratory, Beltsville, MD, United States of America.
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18
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Smith WJM, Liu Y, Simpson SL, Bivins A, Ahmed W. Assessment of nucleic acid extraction protocols for antibiotic resistance genes (ARGs) quantification in aircraft wastewater. Hum Genomics 2024; 18:54. [PMID: 38816866 PMCID: PMC11138010 DOI: 10.1186/s40246-024-00617-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/07/2024] [Indexed: 06/01/2024] Open
Abstract
This study evaluated ten nucleic acid extraction protocols (EP1 to EP10) for measuring five endogenous antibiotic resistance genes (ARGs) in four aircraft wastewater samples (AWW1 to AWW4). The targeted ARGs, including blaCTX-M, blaNDM-1, ermB, qnrS, and tetA, encompassed highly and minimally abundant ARGs. TetA and ermB were consistently detected across four aircraft wastewater samples using the DNeasy Blood and Tissue Kit and the AllPrep PowerViral DNA/RNA kit. QnrS displayed high detection rates with specific extraction protocols and aliquot volumes. Concentrations of ARGs varied across aircraft wastewater samples, with differing extraction protocols influencing quantitative results. The concentrations of tetA, ermB, and qnrS in AWW1 were distinct, while AWW2 to AWW4 exhibited a broader range for tetA, ermB, qnrS, blaCTX-M, and blaNDM-1. EP1 consistently produced the highest concentrations for several ARGs. Collective data analysis revealed varying ARG concentrations across the ten extraction protocols, suggesting the importance of careful extraction protocol selection in ARG monitoring in aircraft wastewater samples. Based on the results, we suggest that a small sample volume (as low as 0.2 mL) may be sufficient for ARG characterization in aircraft wastewater samples. The findings also emphasize the need for considering toilet paper removal without compromising nucleic acid extraction efficiency. The study highlights promising prospects for aircraft wastewater monitoring of ARGs, calling for further investigation into the import and spread of unique ARGs through transport hubs.
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Affiliation(s)
- Wendy J M Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD, 4102, Australia
| | - Yawen Liu
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD, 4102, Australia
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Stuart L Simpson
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD, 4102, Australia
| | - Aaron Bivins
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD, 4102, Australia.
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19
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Calarco J, Pruden A, Harwood VJ. Comparison of methods proposed for monitoring cefotaxime-resistant Escherichia coli in the water environment. Appl Environ Microbiol 2024; 90:e0212823. [PMID: 38572968 PMCID: PMC11107173 DOI: 10.1128/aem.02128-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
Escherichia coli is a promising subject for globally coordinated surveillance of antimicrobial resistance (AMR) in water environments due to its clinical relevance and widespread use as an indicator of fecal contamination. Cefotaxime-resistant E. coli was recently evaluated favorably for this purpose by the World Health Organization TriCycle Protocol, which specifies tryptone bile x-glucuronide (TBX) medium and incubation at 35°C. We assessed comparability with the U.S. Environmental Protection Agency-approved method for E. coli quantification, which uses membrane-thermotolerant E. coli (mTEC) agar and incubation at 44.5°C, in terms of recovery of E. coli and cefotaxime-resistant E. coli from wastewater influent and surface waters. Total E. coli concentrations in wastewater influent were 106-108 CFU/100 mL, while cefotaxime-resistant E. coli were ~100-fold lower. Total E. coli in surface waters were ~102 CFU/100 mL, and cefotaxime-resistant isolates were near the limit of detection (0.4 CFU/100 mL). Total and putative cefotaxime-resistant E. coli concentrations did not differ significantly between media or by incubation method; however, colonies isolated on mTEC were more frequently confirmed to species (97.1%) compared to those from TBX (92.5%). Incubation in a water bath at 44.5°C significantly decreased non-specific background growth and improved confirmation frequency on both media (97.4%) compared to incubation at 35°C (92.3%). This study helps to advance globally coordinated AMR in water environments and suggests that the TriCycle Protocol is adaptable to other standard methods that may be required in different locales, while also offering a means to improve specificity by decreasing the frequency of false-positive identification of cefotaxime-resistant E. coli by modifying incubation conditions.IMPORTANCEAs antibiotic-resistant bacteria in water environments are increasingly recognized as contributors to the global antibiotic resistance crisis, the need for a monitoring subject that captures antibiotic resistance trends on a global scale increases. The World Health Organization TriCycle Protocol proposes the use of cefotaxime-resistant Escherichia coli isolated on tryptone bile x-glucuronide agar. The U.S. Environmental Protection Agency (USEPA) criteria for safe recreational waters also use E. coli as an indicator but specify the use of mTEC agar at a higher incubation temperature (44.5°C vs 35°C). We assessed the comparability of these methods for isolating total and cefotaxime-resistant E. coli, finding overall good agreement and performance, but significantly higher specificity toward E. coli selection with the use of the USEPA incubation protocol and mTEC agar. This study is the first to directly compare these methods and provides evidence that the methods may be used interchangeably for global surveillance of antibiotic resistance in the environment.
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Affiliation(s)
- Jeanette Calarco
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - Valerie J. Harwood
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
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20
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Franklin AM, Weller DL, Durso LM, Bagley M, Davis BC, Frye JG, Grim CJ, Ibekwe AM, Jahne MA, Keely SP, Kraft AL, McConn BR, Mitchell RM, Ottesen AR, Sharma M, Strain EA, Tadesse DA, Tate H, Wells JE, Williams CF, Cook KL, Kabera C, McDermott PF, Garland JL. A one health approach for monitoring antimicrobial resistance: developing a national freshwater pilot effort. FRONTIERS IN WATER 2024; 6:10.3389/frwa.2024.1359109. [PMID: 38855419 PMCID: PMC11157689 DOI: 10.3389/frwa.2024.1359109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Antimicrobial resistance (AMR) is a world-wide public health threat that is projected to lead to 10 million annual deaths globally by 2050. The AMR public health issue has led to the development of action plans to combat AMR, including improved antimicrobial stewardship, development of new antimicrobials, and advanced monitoring. The National Antimicrobial Resistance Monitoring System (NARMS) led by the United States (U.S) Food and Drug Administration along with the U.S. Centers for Disease Control and U.S. Department of Agriculture has monitored antimicrobial resistant bacteria in retail meats, humans, and food animals since the mid 1990's. NARMS is currently exploring an integrated One Health monitoring model recognizing that human, animal, plant, and environmental systems are linked to public health. Since 2020, the U.S. Environmental Protection Agency has led an interagency NARMS environmental working group (EWG) to implement a surface water AMR monitoring program (SWAM) at watershed and national scales. The NARMS EWG divided the development of the environmental monitoring effort into five areas: (i) defining objectives and questions, (ii) designing study/sampling design, (iii) selecting AMR indicators, (iv) establishing analytical methods, and (v) developing data management/analytics/metadata plans. For each of these areas, the consensus among the scientific community and literature was reviewed and carefully considered prior to the development of this environmental monitoring program. The data produced from the SWAM effort will help develop robust surface water monitoring programs with the goal of assessing public health risks associated with AMR pathogens in surface water (e.g., recreational water exposures), provide a comprehensive picture of how resistant strains are related spatially and temporally within a watershed, and help assess how anthropogenic drivers and intervention strategies impact the transmission of AMR within human, animal, and environmental systems.
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Affiliation(s)
- Alison M. Franklin
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Daniel L. Weller
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lisa M. Durso
- U.S. Department of Agriculture, Agricultural Research Service (USDA, ARS), Agroecosystem Management Research, Lincoln, NE, United States
| | - Mark Bagley
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Benjamin C. Davis
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Jonathan G. Frye
- USDA ARS, U.S. National Poultry Research Center, Poultry Microbiological Safety and Processing Research Unit, Athens, GA, United States
| | - Christopher J. Grim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Abasiofiok M. Ibekwe
- USDA, ARS, Agricultural Water Efficiency and Salinity Research Unit, Riverside, CA, United States
| | - Michael A. Jahne
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Scott P. Keely
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Autumn L. Kraft
- Oak Ridge Institute for Science and Education, USDA, ARS, Beltsville, MD, United States
| | - Betty R. McConn
- Oak Ridge Institute for Science and Education, USDA, ARS, Beltsville, MD, United States
| | - Richard M. Mitchell
- Environmental Protection Agency, Office of Water, Washington, DC, United States
| | - Andrea R. Ottesen
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Manan Sharma
- USDA, ARS Environmental Microbial and Food Safety Laboratory, Beltsville, MD, United States
| | - Errol A. Strain
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Daniel A. Tadesse
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Heather Tate
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Jim E. Wells
- USDA, ARS, U.S. Meat Animal Research Center, Meat Safety and Quality, Clay Center, NE, United States
| | - Clinton F. Williams
- USDA, ARS, US Arid-Land Agricultural Research Center, Maricopa, AZ, United States
| | - Kim L. Cook
- USDA, ARS Nutrition, Food Safety and Quality National Program Staff, Beltsville, MD, United States
| | - Claudine Kabera
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Patrick F. McDermott
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Jay L. Garland
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
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21
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Chen C, Li SL, Xu YY, Liu J, Graham DW, Zhu YG. Characterising global antimicrobial resistance research explains why One Health solutions are slow in development: An application of AI-based gap analysis. ENVIRONMENT INTERNATIONAL 2024; 187:108680. [PMID: 38723455 DOI: 10.1016/j.envint.2024.108680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/19/2024]
Abstract
The global health crisis posed by increasing antimicrobial resistance (AMR) implicitly requires solutions based a One Health approach, yet multisectoral, multidisciplinary research on AMR is rare and huge knowledge gaps exist to guide integrated action. This is partly because a comprehensive survey of past research activity has never performed due to the massive scale and diversity of published information. Here we compiled 254,738 articles on AMR using Artificial Intelligence (AI; i.e., Natural Language Processing, NLP) methods to create a database and information retrieval system for knowledge extraction on research perfomed over the last 20 years. Global maps were created that describe regional, methodological, and sectoral AMR research activities that confirm limited intersectoral research has been performed, which is key to guiding science-informed policy solutions to AMR, especially in low-income countries (LICs). Further, we show greater harmonisation in research methods across sectors and regions is urgently needed. For example, differences in analytical methods used among sectors in AMR research, such as employing culture-based versus genomic methods, results in poor communication between sectors and partially explains why One Health-based solutions are not ensuing. Therefore, our analysis suggest that performing culture-based and genomic AMR analysis in tandem in all sectors is crucial for data integration and holistic One Health solutions. Finally, increased investment in capacity development in LICs should be prioritised as they are places where the AMR burden is often greatest. Our open-access database and AI methodology can be used to further develop, disseminate, and create new tools and practices for AMR knowledge and information sharing.
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Affiliation(s)
- Cai Chen
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shu-Le Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao-Yang Xu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Jue Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China; Institute for Global Health and Development, Peking University, Beijing 100191, China
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle, UK.
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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22
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Mondal AH, Khare K, Saxena P, Debnath P, Mukhopadhyay K, Yadav D. A Review on Colistin Resistance: An Antibiotic of Last Resort. Microorganisms 2024; 12:772. [PMID: 38674716 PMCID: PMC11051878 DOI: 10.3390/microorganisms12040772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Antibiotic resistance has emerged as a significant global public health issue, driven by the rapid adaptation of microorganisms to commonly prescribed antibiotics. Colistin, previously regarded as a last-resort antibiotic for treating infections caused by Gram-negative bacteria, is increasingly becoming resistant due to chromosomal mutations and the acquisition of resistance genes carried by plasmids, particularly the mcr genes. The mobile colistin resistance gene (mcr-1) was first discovered in E. coli from China in 2016. Since that time, studies have reported different variants of mcr genes ranging from mcr-1 to mcr-10, mainly in Enterobacteriaceae from various parts of the world, which is a major concern for public health. The co-presence of colistin-resistant genes with other antibiotic resistance determinants further complicates treatment strategies and underscores the urgent need for enhanced surveillance and antimicrobial stewardship efforts. Therefore, understanding the mechanisms driving colistin resistance and monitoring its global prevalence are essential steps in addressing the growing threat of antimicrobial resistance and preserving the efficacy of existing antibiotics. This review underscores the critical role of colistin as a last-choice antibiotic, elucidates the mechanisms of colistin resistance and the dissemination of resistant genes, explores the global prevalence of mcr genes, and evaluates the current detection methods for colistin-resistant bacteria. The objective is to shed light on these key aspects with strategies for combating the growing threat of resistance to antibiotics.
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Affiliation(s)
- Aftab Hossain Mondal
- Department of Microbiology, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary University, Gurugram 122505, Haryana, India; (A.H.M.); (P.D.)
| | - Kriti Khare
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Prachika Saxena
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Parbati Debnath
- Department of Microbiology, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary University, Gurugram 122505, Haryana, India; (A.H.M.); (P.D.)
| | - Kasturi Mukhopadhyay
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Dhananjay Yadav
- Department of Life Science, Yeungnam University, Gyeongsan 712-749, Republic of Korea
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23
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Arnal C, Belhadj-Kaabi F, Ingrand V. [Which contribution of wastewater treatment plants in the fight against antimicrobial resistance?]. C R Biol 2024; 346:23-33. [PMID: 37655905 DOI: 10.5802/crbiol.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/21/2023] [Indexed: 09/02/2023]
Abstract
Due to the massive use of antibiotics, antimicrobial resistance (AMR) continues to spread, endangering global disease control and environmental quality. The sources of bacteria or antimicrobial resistance genes are linked to human activities: urban, hospital and industrial discharges, livestock farms). The role of sanitation systems-sewerage, wastewater treatment and sludge treatment (WWTP)-in the problem of AMR has not yet been clearly established by the scientific community. The data available to date show that they eliminate part of the bacteria, genes and antibiotics, although this is not their primary vocation. WWTPs thus play an important filtering role to limit dissemination in the environment. On the other hand, some authors warn against their potential involvement in the selection of new resistant germs, given the conditions conducive to the exchange of genetic material between microbial strains of various types and exposed to selective agents. Today, knowledge of the mechanisms involved in the selection of antibiotic resistance and the fate of bacteria and resistance genes within sanitation systems remains limited. Research is needed to better characterize the contribution of wastewater systems and the performance of wastewater, recycled water, stormwater and sludge treatment processes.
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24
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Capone D, Cumming O, Flemister A, Ilevbare V, Irish SR, Keenum I, Knee J, Nala R, Brown J. Sanitation in urban areas may limit the spread of antimicrobial resistance via flies. PLoS One 2024; 19:e0298578. [PMID: 38507457 PMCID: PMC10954131 DOI: 10.1371/journal.pone.0298578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/28/2024] [Indexed: 03/22/2024] Open
Abstract
Synanthropic filth flies are common where sanitation is poor and fecal wastes are accessible to them. These flies have been proposed as mechanical vectors for the localized transport of fecal microbes including antimicrobial resistant (AMR) organisms and associated antimicrobial resistance genes (ARGs), increasing exposure risks. We evaluated whether an onsite sanitation intervention in Maputo, Mozambique reduced the concentration of enteric bacteria and the frequency of detection of ARGs carried by flies collected in household compounds of low-income neighborhoods. Additionally, we assessed the phenotypic resistance profile of Enterobacteriaceae isolates recovered from flies during the pre-intervention phase. After fly enumeration at study compounds, quantitative polymerase chain reaction was used to quantify an enteric 16S rRNA gene (i.e., specific to a cluster of phylotypes corresponding to 5% of the human fecal microflora), 28 ARGs, and Kirby Bauer Disk Diffusion of Enterobacteriaceae isolates was utilized to assess resistance to eleven clinically relevant antibiotics. The intervention was associated with a 1.5 log10 reduction (95% confidence interval: -0.73, -2.3) in the concentration of the enteric 16S gene and a 31% reduction (adjusted prevalence ratio = 0.69, [0.52, 0.92]) in the mean number of ARGs per fly compared to a control group with poor sanitation. This protective effect was consistent across the six ARG classes that we detected. Enterobacteriaceae isolates-only from the pre-intervention phase-were resistant to a mean of 3.4 antibiotics out of the eleven assessed. Improving onsite sanitation infrastructure in low-income informal settlements may help reduce fly-mediated transmission of enteric bacteria and the ARGs carried by them.
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Affiliation(s)
- Drew Capone
- Department of Environmental and Occupational Health, Indiana University, Bloomington, Indiana, United States of America
| | - Oliver Cumming
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Abeoseh Flemister
- Roy Blunt NextGen Precision Health, University of Missouri, Columbia, Missouri, United States of America
- Department of Radiology, University of Missouri, Columbia, MO, United States of America
| | - Victor Ilevbare
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Seth R. Irish
- Epidemiology and Public Health Department, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
| | - Ishi Keenum
- Department of Civil, Environmental and Geospatial Engineering, Michigan Technological University, Houghton, Michigan, United States of America
| | - Jackie Knee
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Rassul Nala
- Ministério da Saúde de Moçambique, Instituto Nacional de Saúde, Maputo, Mozambique
| | - Joe Brown
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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25
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Singh D, Pal S, Subramanian S, Manickam N. Comparative genomics of an extensively drug resistant strain Klebsiella pneumoniae IITR008 with international high-risk clonal lineage ST147 isolated from river water. Antonie Van Leeuwenhoek 2024; 117:57. [PMID: 38491220 DOI: 10.1007/s10482-024-01955-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 02/26/2024] [Indexed: 03/18/2024]
Abstract
Carbapenem resistant Klebsiella pneumoniae causing severe infection resulting in morbidity and mortality have become a global health concern. K. pneumoniae with sequence type ST147 is an international high-risk clonal lineage, genomic studies have been done on K. pneumoniae ST147 isolated from clinical origin but genomic data for environmental K. pneumoniae ST147 is very scarce. Herein, K. pneumoniae IITR008, an extensively drug resistant and potentially hypervirulent bacterium, was isolated from Triveni Sangam, the confluence of three rivers where religious congregations are organized. Phenotypic, genomic and comparative genomic analysis of strain IITR008 was performed. Antibiotic susceptibility profiling revealed resistance to 9 different classes of antibiotics including ß-lactams, ß-lactam combination agents, carbapenem, aminoglycoside, macrolide, quinolones, cephams, phenicol, and folate pathway antagonists and was found to be susceptible to only tetracycline. The strain IITR008 possesses hypervirulence genes namely, iutA and iroN in addition to numerous virulence factors coding for adherence, regulation, iron uptake, secretion system and toxin. Both the IITR008 chromosome and plasmid pIITR008_75 possess a plethora of clinically relevant antibiotic-resistant genes (ARGs) including blaCTX-M-15, blaTEM-1, and blaSHV-11, corroborating the phenotypic resistance. Comparative genomic analysis with other ST147 K. pneumoniae provided insights on the phylogenetic clustering of IITR008 with a clinical strain isolated from a patient in Czech with recent travel history in India and other clinical strains isolated from India and Pakistan. According to the 'One Health' perspective, surveillance of antibiotic resistance in the environment is crucial to impede its accelerated development in diverse ecological niches.
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Affiliation(s)
- Deeksha Singh
- Environmental Biotechnology Laboratory, Environmental Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Shilpee Pal
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Srikrishna Subramanian
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Natesan Manickam
- Environmental Biotechnology Laboratory, Environmental Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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Schachner-Groehs I, Koller M, Leopold M, Kolm C, Linke RB, Jakwerth S, Kolarević S, Kračun-Kolarević M, Kandler W, Sulyok M, Vierheilig J, Toumi M, Farkas R, Toth E, Kittinger C, Zarfel G, Farnleitner AH, Kirschner AKT. Linking antibiotic resistance gene patterns with advanced faecal pollution assessment and environmental key parameters along 2300 km of the Danube River. WATER RESEARCH 2024; 252:121244. [PMID: 38340455 DOI: 10.1016/j.watres.2024.121244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
The global spread of antimicrobial resistance (AMR) in the environment is a growing health threat. Large rivers are of particular concern as they are highly impacted by wastewater discharge while being vital lifelines serving various human needs. A comprehensive understanding of occurrence, spread and key drivers of AMR along whole river courses is largely lacking. We provide a holistic approach by studying spatiotemporal patterns and hotspots of antibiotic resistance genes (ARGs) along 2311 km of the navigable Danube River, combining a longitudinal and temporal monitoring campaign. The integration of advanced faecal pollution diagnostics and environmental and chemical key parameters allowed linking ARG concentrations to the major pollution sources and explaining the observed patterns. Nine AMR markers, including genes conferring resistance to five different antibiotic classes of clinical and environmental relevance, and one integrase gene were determined by probe-based qPCR. All AMR targets could be quantified in Danube River water, with intI1 and sul1 being ubiquitously abundant, qnrS, tetM, blaTEM with intermediate abundance and blaOXA-48like, blaCTX-M-1 group, blaCTX-M-9 group and blaKPC genes with rare occurrence. Human faecal pollution from municipal wastewater discharges was the dominant factor shaping ARG patterns along the Danube River. Other significant correlations of specific ARGs were observed with discharge, certain metals and pesticides. In contrast, intI1 was not associated with wastewater but was already established in the water microbiome. Animal contamination was detected only sporadically and was correlated with ARGs only in the temporal sampling set. During temporal monitoring, an extraordinary hotspot was identified emphasizing the variability within natural waters. This study provides the first comprehensive baseline concentrations of ARGs in the Danube River and lays the foundation for monitoring future trends and evaluating potential reduction measures. The applided holistic approach proved to be a valuable methodological contribution towards a better understanding of the environmental occurrence of AMR.
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Affiliation(s)
- Iris Schachner-Groehs
- Institute of Hygiene and Applied Immunology - Water Microbiology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Kinderspitalgasse 15, Vienna 1090, Austria
| | - Michael Koller
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Neue Stiftingtalstraße 6, Graz 8010, Austria
| | - Melanie Leopold
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr.-Karl-Dorrek-Straße 30, Krems an der Donau 3500, Austria
| | - Claudia Kolm
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr.-Karl-Dorrek-Straße 30, Krems an der Donau 3500, Austria; Institute of Chemical, Environmental and Bioscience Engineering, Research Group Microbiology and Molecular Diagnostics, Technische Universität Wien, Gumpendorfer Straße 1A/166, Vienna 1060, Austria
| | - Rita B Linke
- Institute of Chemical, Environmental and Bioscience Engineering, Research Group Microbiology and Molecular Diagnostics, Technische Universität Wien, Gumpendorfer Straße 1A/166, Vienna 1060, Austria
| | - Stefan Jakwerth
- Institute of Hygiene and Applied Immunology - Water Microbiology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Kinderspitalgasse 15, Vienna 1090, Austria
| | - Stoimir Kolarević
- Department of Hydroecology and Water Protection, Institute for Biological Research ¨Siniša Stanković¨, National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade 11060, Serbia
| | - Margareta Kračun-Kolarević
- Department of Hydroecology and Water Protection, Institute for Biological Research ¨Siniša Stanković¨, National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade 11060, Serbia
| | - Wolfgang Kandler
- Department of Agrotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Konrad-Lorenz-Straße 20, Tulln an der Donau 3430, Austria
| | - Michael Sulyok
- Department of Agrotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Konrad-Lorenz-Straße 20, Tulln an der Donau 3430, Austria
| | - Julia Vierheilig
- Institute of Water Quality and Resource Management, Technische Universität Wien, Karlsplatz 13/226-1, Wien 1040, Austria
| | - Marwene Toumi
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C., H-1117, Budapest, Hungary
| | - Rózsa Farkas
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C., H-1117, Budapest, Hungary
| | - Erika Toth
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C., H-1117, Budapest, Hungary
| | - Clemens Kittinger
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Neue Stiftingtalstraße 6, Graz 8010, Austria
| | - Gernot Zarfel
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Neue Stiftingtalstraße 6, Graz 8010, Austria
| | - Andreas H Farnleitner
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr.-Karl-Dorrek-Straße 30, Krems an der Donau 3500, Austria; Institute of Chemical, Environmental and Bioscience Engineering, Research Group Microbiology and Molecular Diagnostics, Technische Universität Wien, Gumpendorfer Straße 1A/166, Vienna 1060, Austria.
| | - A K T Kirschner
- Institute of Hygiene and Applied Immunology - Water Microbiology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Kinderspitalgasse 15, Vienna 1090, Austria; Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr.-Karl-Dorrek-Straße 30, Krems an der Donau 3500, Austria.
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Li Y, Li R, Hou J, Sun X, Wang Y, Li L, Yang F, Yao Y, An Y. Mobile genetic elements affect the dissemination of antibiotic resistance genes (ARGs) of clinical importance in the environment. ENVIRONMENTAL RESEARCH 2024; 243:117801. [PMID: 38043895 DOI: 10.1016/j.envres.2023.117801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
The prevalence of antibiotic resistance genes (ARGs) in the environment is a quintessential One Health issue that threats both human and ecosystem health; however, the source and transmission of ARGs, especially clinically important ARGs (CLIARGs), in the environment have not yet been well studied. In the present study, shotgun metagenomic approaches were used to characterize the microbiome, resistome, and mobilome composition in human feces and six different environment sample types in South China. Overall, the resistome harbored 157 CLIARGs, with specific ARG hotspots (e.g., human feces, wastewater treatment plants, livestock manure and wastewater) excreting significantly higher abundance of CLIARGs compared with the natural environment. A redundancy analysis (RDA) was performed and revealed that the bacterial community compositions and mobile genetic elements (MGEs) explained 55.08% and 34.68% of the variations in ARG abundance, respectively, indicating that both bacterial community and MGEs are key contributors to the maintenance and dissemination of CLIARGs in the environment. The network analysis revealed non-random co-occurrence patterns between 200 bacterial genera and 147 CLIARGs, as well as between 135 MGEs and 123 CLIARGs. In addition to numerous co-shared CLIARGs among different sample types, the source tracking program based on the FEAST probabilistic model was used to estimate the relative contributions of the CLIARGs from potential sources to the natural environment. The source tracking analysis results delineated that mobilome, more than microbiome, contributed CLIARG transmission from those ARG hotspots into natural environment, and the MGEs in WWTPs seem to play the most significant role in the spread of CLIARGs to the natural environment (average contribution 32.9%-46.4%). Overall, this study demonstrated the distribution and dissemination of CLIARGs in the environment, and aimed to better inform strategies to control the spread of CLIARGs into the natural environment.
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Affiliation(s)
- Ye Li
- School of Environment Science and Engineering, Tianjin University, Tianjin, 300350, China; Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Ruilin Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Jie Hou
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
| | - Xuan Sun
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yajun Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Linyun Li
- Ministry of Social and Ecological Civilization, Party School of Hebei Provincial Committee of C.P.C, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yanpo Yao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
| | - Yi An
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
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28
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Rybak D, Rinoldi C, Nakielski P, Du J, Haghighat Bayan MA, Zargarian SS, Pruchniewski M, Li X, Strojny-Cieślak B, Ding B, Pierini F. Injectable and self-healable nano-architectured hydrogel for NIR-light responsive chemo- and photothermal bacterial eradication. J Mater Chem B 2024; 12:1905-1925. [PMID: 38305576 DOI: 10.1039/d3tb02693k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Hydrogels with multifunctional properties activated at specific times have gained significant attention in the biomedical field. As bacterial infections can cause severe complications that negatively impact wound repair, herein, we present the development of a stimuli-responsive, injectable, and in situ-forming hydrogel with antibacterial, self-healing, and drug-delivery properties. In this study, we prepared a Pluronic F-127 (PF127) and sodium alginate (SA)-based hydrogel that can be targeted to a specific tissue via injection. The PF127/SA hydrogel was incorporated with polymeric short-filaments (SFs) containing an anti-inflammatory drug - ketoprofen, and stimuli-responsive polydopamine (PDA) particles. The hydrogel, after injection, could be in situ gelated at the body temperature, showing great in vitro stability and self-healing ability after 4 h of incubation. The SFs and PDA improved the hydrogel injectability and compressive strength. The introduction of PDA significantly accelerated the KET release under near-infrared light exposure and extended its release validity period. The excellent composites' photo-thermal performance led to antibacterial activity against representative Gram-positive and Gram-negative bacteria, resulting in 99.9% E. coli and S. aureus eradication after 10 min of NIR light irradiation. In vitro, fibroblast L929 cell studies confirmed the materials' biocompatibility and paved the way toward further in vivo and clinical application of the system for chronic wound treatments.
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Affiliation(s)
- Daniel Rybak
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw 02-106, Poland.
| | - Chiara Rinoldi
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw 02-106, Poland.
| | - Paweł Nakielski
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw 02-106, Poland.
| | - Jingtao Du
- Innovation Center for Textile Science and Technology, Collage of Textiles, Donghua University, Shanghai 201620, China
| | - Mohammad Ali Haghighat Bayan
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw 02-106, Poland.
| | - Seyed Shahrooz Zargarian
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw 02-106, Poland.
| | - Michał Pruchniewski
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw 02-787, Poland
| | - Xiaoran Li
- Innovation Center for Textile Science and Technology, Collage of Textiles, Donghua University, Shanghai 201620, China
| | - Barbara Strojny-Cieślak
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw 02-787, Poland
| | - Bin Ding
- Innovation Center for Textile Science and Technology, Collage of Textiles, Donghua University, Shanghai 201620, China
| | - Filippo Pierini
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw 02-106, Poland.
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29
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Rodger G, Chau K, Aranega-Bou P, Roohi A, Moore G, Hopkins KL, Hopkins S, Walker AS, Stoesser N. A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing. J Hosp Infect 2024; 144:128-136. [PMID: 38145816 DOI: 10.1016/j.jhin.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Hospital sinks are environmental reservoirs that harbour healthcare-associated (HCA) pathogens. Selective pressures in sink environments, such as antibiotic residues, nutrient waste and hardness ions, may promote antibiotic resistance gene (ARG) exchange between bacteria. However, cheap and accurate sampling methods to characterize these factors are lacking. AIMS To validate a workflow to detect antibiotic residues and evaluate water chemistry using dipsticks. Secondarily, to validate boric acid to preserve the taxonomic and ARG ('resistome') composition of sink trap samples for metagenomic sequencing. METHODS Antibiotic residue dipsticks were validated against serial dilutions of ampicillin, doxycycline, sulfamethoxazole and ciprofloxacin, and water chemistry dipsticks against serial dilutions of chemical calibration standards. Sink trap aspirates were used for a 'real-world' pilot evaluation of dipsticks. To assess boric acid as a preservative of microbial diversity, the impact of incubation with and without boric acid at ∼22 °C on metagenomic sequencing outputs was evaluated at Day 2 and Day 5 compared with baseline (Day 0). FINDINGS The limits of detection for each antibiotic were: 3 μg/L (ampicillin), 10 μg/L (doxycycline), 20 μg/L (sulfamethoxazole) and 8 μg/L (ciprofloxacin). The best performing water chemistry dipstick correctly characterized 34/40 (85%) standards in a concentration-dependent manner. One trap sample tested positive for the presence of tetracyclines and sulphonamides. Taxonomic and resistome composition were largely maintained after storage with boric acid at ∼22 °C for up to five days. CONCLUSIONS Dipsticks can be used to detect antibiotic residues and characterize water chemistry in sink trap samples. Boric acid was an effective preservative of trap sample composition, representing a low-cost alternative to cold-chain transport.
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Affiliation(s)
- G Rodger
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK
| | - K Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK
| | - P Aranega-Bou
- Biosafety, Air and Water Microbiology Group, UK Health Security Agency, Porton Down, UK
| | - A Roohi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK
| | - G Moore
- Biosafety, Air and Water Microbiology Group, UK Health Security Agency, Porton Down, UK
| | | | - S Hopkins
- UK Health Security Agency, Colindale, UK
| | - A S Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - N Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
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30
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Djordjevic SP, Jarocki VM, Seemann T, Cummins ML, Watt AE, Drigo B, Wyrsch ER, Reid CJ, Donner E, Howden BP. Genomic surveillance for antimicrobial resistance - a One Health perspective. Nat Rev Genet 2024; 25:142-157. [PMID: 37749210 DOI: 10.1038/s41576-023-00649-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2023] [Indexed: 09/27/2023]
Abstract
Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.
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Affiliation(s)
- Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia.
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia.
| | - Veronica M Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Torsten Seemann
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Anne E Watt
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Barbara Drigo
- UniSA STEM, University of South Australia, Adelaide, South Australia, Australia
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Ethan R Wyrsch
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Cameron J Reid
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
- Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, South Australia, Australia
| | - Benjamin P Howden
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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Corrin T, Rabeenthira P, Young KM, Mathiyalagan G, Baumeister A, Pussegoda K, Waddell LA. A scoping review of human pathogens detected in untreated human wastewater and sludge. JOURNAL OF WATER AND HEALTH 2024; 22:436-449. [PMID: 38421635 PMCID: wh_2024_326 DOI: 10.2166/wh.2024.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Wastewater monitoring is an approach to identify the presence or abundance of pathogens within a population. The objective of this scoping review (ScR) was to identify and characterize research on human pathogens and antimicrobial resistance detected in untreated human wastewater and sludge. A search was conducted up to March 2023 and standard ScR methodology was followed. This ScR included 1,722 articles, of which 56.5% were published after the emergence of COVID-19. Viruses and bacteria were commonly investigated, while research on protozoa, helminths, and fungi was infrequent. Articles prior to 2019 were dominated by research on pathogens transmitted through fecal-oral or waterborne pathways, whereas more recent articles have explored the detection of pathogens transmitted through other pathways such as respiratory and vector-borne. There was variation in sampling, samples, and sample processing across studies. The current evidence suggests that wastewater monitoring could be applied to a range of pathogens as a public health tool to detect an emerging pathogen and understand the burden and spread of disease to inform decision-making. Further development and refinement of the methods to identify and interpret wastewater signals for different prioritized pathogens are needed to develop standards on when, why, and how to monitor effectively.
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Affiliation(s)
- Tricia Corrin
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, 370 Speedvale Avenue West, Guelph, Ontario N1H 7M7, Canada E-mail:
| | - Prakathesh Rabeenthira
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, 110 Stone Road, Guelph, Ontario N1G 3W4, Canada
| | - Kaitlin M Young
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, 370 Speedvale Avenue West, Guelph, Ontario N1H 7M7, Canada
| | - Gajuna Mathiyalagan
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, 110 Stone Road, Guelph, Ontario N1G 3W4, Canada
| | - Austyn Baumeister
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, 370 Speedvale Avenue West, Guelph, Ontario N1H 7M7, Canada
| | - Kusala Pussegoda
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, 370 Speedvale Avenue West, Guelph, Ontario N1H 7M7, Canada
| | - Lisa A Waddell
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, 370 Speedvale Avenue West, Guelph, Ontario N1H 7M7, Canada
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Philo SE, De León KB, Noble RT, Zhou NA, Alghafri R, Bar-Or I, Darling A, D'Souza N, Hachimi O, Kaya D, Kim S, Gaardbo Kuhn K, Layton BA, Mansfeldt C, Oceguera B, Radniecki TS, Ram JL, Saunders LP, Shrestha A, Stadler LB, Steele JA, Stevenson BS, Vogel JR, Bibby K, Boehm AB, Halden RU, Delgado Vela J. Wastewater surveillance for bacterial targets: current challenges and future goals. Appl Environ Microbiol 2024; 90:e0142823. [PMID: 38099657 PMCID: PMC10807411 DOI: 10.1128/aem.01428-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024] Open
Abstract
Wastewater-based epidemiology (WBE) expanded rapidly in response to the COVID-19 pandemic. As the public health emergency has ended, researchers and practitioners are looking to shift the focus of existing wastewater surveillance programs to other targets, including bacteria. Bacterial targets may pose some unique challenges for WBE applications. To explore the current state of the field, the National Science Foundation-funded Research Coordination Network (RCN) on Wastewater Based Epidemiology for SARS-CoV-2 and Emerging Public Health Threats held a workshop in April 2023 to discuss the challenges and needs for wastewater bacterial surveillance. The targets and methods used in existing programs were diverse, with twelve different targets and nine different methods listed. Discussions during the workshop highlighted the challenges in adapting existing programs and identified research gaps in four key areas: choosing new targets, relating bacterial wastewater data to human disease incidence and prevalence, developing methods, and normalizing results. To help with these challenges and research gaps, the authors identified steps the larger community can take to improve bacteria wastewater surveillance. This includes developing data reporting standards and method optimization and validation for bacterial programs. Additionally, more work is needed to understand shedding patterns for potential bacterial targets to better relate wastewater data to human infections. Wastewater surveillance for bacteria can help provide insight into the underlying prevalence in communities, but much work is needed to establish these methods.IMPORTANCEWastewater surveillance was a useful tool to elucidate the burden and spread of SARS-CoV-2 during the pandemic. Public health officials and researchers are interested in expanding these surveillance programs to include bacterial targets, but many questions remain. The NSF-funded Research Coordination Network for Wastewater Surveillance of SARS-CoV-2 and Emerging Public Health Threats held a workshop to identify barriers and research gaps to implementing bacterial wastewater surveillance programs.
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Affiliation(s)
- Sarah E. Philo
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Kara B. De León
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma, USA
| | - Rachel T. Noble
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, North Carolina, USA
| | - Nicolette A. Zhou
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Rashed Alghafri
- International Center for Forensic Sciences, Dubai Police, Dubai, UAE
| | - Itay Bar-Or
- Israel Ministry of Health, Jerusalem, Israel
| | - Amanda Darling
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA
| | - Oumaima Hachimi
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA
| | - Devrim Kaya
- School of Public Health, San Diego State University, San Diego, California, USA
| | - Sooyeol Kim
- Department of Civil and Environmental Engineering, University of California Berkeley, Berkeley, California, USA
| | - Katrin Gaardbo Kuhn
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | | | - Cresten Mansfeldt
- Environmental Engineering Program, University of Colorado Boulder, Boulder, Colorado, USA
| | - Bethany Oceguera
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Tyler S. Radniecki
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA
| | - Jeffrey L. Ram
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | | | - Abhilasha Shrestha
- Environmental and Occupational Health Sciences Division, University of Illinois Chicago School of Public Health, Chicago, Illinois, USA
| | - Lauren B. Stadler
- Civil and Environmental Engineering, Rice University, Houston, Texas, USA
| | - Joshua A. Steele
- Department of Microbiology, Southern California Coastal Research Project, Costa Mesa, California, USA
| | | | - Jason R. Vogel
- School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | - Rolf U. Halden
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
| | - Jeseth Delgado Vela
- Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina, USA
- Department of Civil and Environmental Engineering, Howard University, Washington, District of Columbia, USA
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Sun X, Wang X, Han Q, Yu Q, Wanyan R, Li H. Bibliometric analysis of papers on antibiotic resistance genes in aquatic environments on a global scale from 2012 to 2022: Evidence from universality, development and harmfulness. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168597. [PMID: 37981129 DOI: 10.1016/j.scitotenv.2023.168597] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023]
Abstract
Antibiotic resistance genes (ARGs), emerging pollutants, are widely distributed in aquatic environments, and are tightly linked to human health. However, the research progress and trends in recent years on ARGs of aquatic environments are still unclear. This paper made a comprehensive understanding of the research advance, study trends and key topics of 1592 ARGs articles from 2012 to 2022 by bibliometrics. Publications on ARGs increased rapidly from 2012 to 2022, and scholars paid closer attention to the field of Environmental Sciences & Ecology. The most influential country and institution was mainly China and Chinese Academy of Sciences, respectively. The most articles (14.64 %) were published in the journal Science of the total environment. China and USA had the most cooperation, and USA was more inclined to international cooperation. PCR-based methods for water ARG research were the most widely used, followed by metagenomics. The most studied ARG types were sulfonamides, tetracyclines. Moreover, ARGs from wastewater and rivers were popularly concerned. Current topics mainly included pollution investigation, characteristics, transmission, reduction and risk identification of ARGs. Additionally, future research directions were proposed. Generally, by bibliometrics, this paper reviews the research hotspots and future directions of ARGs on a global scale, and summarizes the more important categories of ARGs, the pollution degree of ARGs in the relevant water environment and the research methods, which can provide a more comprehensive information for the future breakthrough of resistance mechanism, prevention and control standard formulation of ARGs.
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Affiliation(s)
- Xiaofang Sun
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiaochen Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Ruijun Wanyan
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China.
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Batantou Mabandza D, Colletin E, Dagot C, Quétel I, Breurec S, Guyomard-Rabenirina S. Do Microorganisms in Bathing Water in Guadeloupe (French West Indies) Have Resistance Genes? Antibiotics (Basel) 2024; 13:87. [PMID: 38247646 PMCID: PMC10812525 DOI: 10.3390/antibiotics13010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
Waterborne faecal contamination is a major public health concern. The main objectives of this study were to investigate faecal contamination and Escherichia coli (E. coli) antibiotic resistance in recreational fresh water from Guadeloupe and to characterise the microbiome and resistome composition in biofilms from submerged rocks. Significant faecal contamination was observed at 14 freshwater sites. E. coli predominated (62%), followed by Enterobacter cloacae (11%) and Acinetobacter spp. (11%). Of 152 E. coli isolated, none produced extended-spectrum beta-lactamases (ESBLs), but 7% showed resistance to streptomycin and 4% to tetracycline. Biofilm resistome analysis revealed clinically significant antibiotic-resistance genes (ARGs), including those coding for resistance to sulfonamides (sul1), carbapenems (blaKPC), and third-generation cephalosporins (blaCTX-M). Mobile genetic elements (MGEs) (intI1, intI2, intI3) linked to resistance to aminoglycosides, beta-lactams, tetracycline, as well as heavy metal resistance determinants (copA, cusF, czcA, merA) conferring resistance to copper, silver, cadmium, and mercury were also detected. Diverse bacterial phyla were found in biofilm samples, of which Proteobacteria, Bacteroidetes, Planctonomycetes, and Cyanobacteria were predominant. Despite the frequent presence of E. coli exceeding regulatory standards, the low levels of antibiotic-resistant bacteria in freshwater and of ARGs and MGEs in associated biofilms suggest limited antibiotic resistance in Guadeloupean recreational waters.
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Affiliation(s)
- Degrâce Batantou Mabandza
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
| | - Edlyne Colletin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
| | - Christophe Dagot
- University of Limoges, INSERM, CHU Limoges, RESINFIT, U1092, 87000 Limoges, France
| | - Isaure Quétel
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
| | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
- Faculty of Medicine Hyacinthe Bastaraud, University of the Antilles, 97110 Pointe-à-Pitre, France
- INSERM, Centre for Clinical Investigation 1424, 97110 Pointe-à-Pitre, France
- Department of Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, 34394 Montpellier, France
- Laboratory of Clinical Microbiology, University Hospital Centre of Guadeloupe, 971110 Pointe-à-Pitre, France
| | - Stéphanie Guyomard-Rabenirina
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
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Saleem F, Li E, Edge TA, Tran KL, Schellhorn HE. Identification of potential microbial risk factors associated with fecal indicator exceedances at recreational beaches. ENVIRONMENTAL MICROBIOME 2024; 19:4. [PMID: 38225663 PMCID: PMC10790499 DOI: 10.1186/s40793-024-00547-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024]
Abstract
BACKGROUND Fecal bacterial densities are proxy indicators of beach water quality, and beach posting decisions are made based on Beach Action Value (BAV) exceedances for a beach. However, these traditional beach monitoring methods do not reflect the full extent of microbial water quality changes associated with BAV exceedances at recreational beaches (including harmful cyanobacteria). This proof of concept study evaluates the potential of metagenomics for comprehensively assessing bacterial community changes associated with BAV exceedances compared to non-exceedances for two urban beaches and their adjacent river water sources. RESULTS Compared to non-exceedance samples, BAV exceedance samples exhibited higher alpha diversity (diversity within the sample) that could be further differentiated into separate clusters (Beta-diversity). For Beach A, Cyanobacterial sequences (resolved as Microcystis and Pseudanabaena at genus level) were significantly more abundant in BAV non-exceedance samples. qPCR validation supported the Cyanobacterial abundance results from metagenomic analysis and also identified saxitoxin genes in 50% of the non-exceedance samples. Microcystis sp and saxitoxin gene sequences were more abundant on non-exceedance beach days (when fecal indicator data indicated the beach should be open for water recreational purposes). For BAV exceedance days, Fibrobacteres, Pseudomonas, Acinetobacter, and Clostridium sequences were significantly more abundant (and positively correlated with fecal indicator densities) for Beach A. For Beach B, Spirochaetes (resolved as Leptospira on genus level) Burkholderia and Vibrio sequences were significantly more abundant in BAV exceedance samples. Similar bacterial diversity and abundance trends were observed for river water sources compared to their associated beaches. Antibiotic Resistance Genes (ARGs) were also consistently detected at both beaches. However, we did not observe a significant difference or correlation in ARGs abundance between BAV exceedance and non-exceedance samples. CONCLUSION This study provides a more comprehensive analysis of bacterial community changes associated with BAV exceedances for recreational freshwater beaches. While there were increases in bacterial diversity and some taxa of potential human health concern associated with increased fecal indicator densities and BAV exceedances (e.g. Pseudomonas), metagenomics analyses also identified other taxa of potential human health concern (e.g. Microcystis) associated with lower fecal indicator densities and BAV non-exceedances days. This study can help develop more targeted beach monitoring strategies and beach-specific risk management approaches.
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Affiliation(s)
- Faizan Saleem
- Department of Biology, McMaster University, 1280 Main St W., Hamilton, ON, L8S 4L8, Canada
| | - Enze Li
- Department of Biology, McMaster University, 1280 Main St W., Hamilton, ON, L8S 4L8, Canada
| | - Thomas A Edge
- Department of Biology, McMaster University, 1280 Main St W., Hamilton, ON, L8S 4L8, Canada
| | - Kevin L Tran
- Department of Biology, McMaster University, 1280 Main St W., Hamilton, ON, L8S 4L8, Canada
| | - Herb E Schellhorn
- Department of Biology, McMaster University, 1280 Main St W., Hamilton, ON, L8S 4L8, Canada.
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Gholipour S, Shamsizadeh Z, Halabowski D, Gwenzi W, Nikaeen M. Combating antibiotic resistance using wastewater surveillance: Significance, applications, challenges, and future directions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168056. [PMID: 37914125 DOI: 10.1016/j.scitotenv.2023.168056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 11/03/2023]
Abstract
The global increase of antibiotic resistance (AR) and resistant infections call for effective surveillance methods for understanding and mitigating (re)-emerging public health risks. Wastewater surveillance (WS) of antibiotic resistance is an emerging, but currently under-utilized decision-support tool in public health systems. Recent years have witnessed an increase in evidence linking antibiotic resistance in wastewaters to that of the community. To date, very few comprehensive reviews exist on the application of WS to understand AR and resistant infections in population. Current and emerging AR detection methods, and their merits and limitations are discussed. Wastewater surveillance has several merits relative to individual testing, including; (1) low per capita testing cost, (2) high spatial coverage, (3) low requirement for diagnostic equipment, and (4) detection of health threats ahead of real outbreaks. The applications of WS as an early warning system and decision support tool to understand and mitigate AR are discussed. Wastewater surveillance could be a tool of choice in low-income settings lacking resources and diagnostic facilities for individual testing. To demonstrate the utility of WS, empirical evidence from field case studies is presented. However, constraints still exist, including; (1) lack of standardized protocols, (2) the clinical utility and sensitivity of WS-based data, (3) uncertainties in relating WS data to pathogenic and virulent bacteria, and (4) whether or not AR in stools and ultimately wastewater represent the complete human resistome. Finally, further prospects are presented, include knowledge gaps on; (1) development of low-cost biosensors for AR, (2) development of WS protocols (sampling, processing, interpretation), (3) further pilot scale studies to understand the opportunities and limits of WS, and (4) development of computer-based analytical tools to facilitate rapid data collection, visualization and interpretation. Therefore, the present paper discusses the principles, opportunities, and constraints of wastewater surveillance applications to understand AR and safeguard public health.
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Affiliation(s)
- Sahar Gholipour
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zahra Shamsizadeh
- Department of Environmental Health Engineering, School of Health, Larestan University of Medical Sciences, Larestan, Iran
| | - Dariusz Halabowski
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Ecology and Vertebrate Zoology, Lodz, Poland
| | - Willis Gwenzi
- Universität Kassel, Fachbereich Ökologische Agrarwissenschaften Fachgebiet Grünlandwissenschaft und Nachwachsende Rohstoffe, Steinstr. 19, 37249 Witzenhausen, Germany; Leibniz-Institut für Agrartechnik und Bioökonomie e.V. Max-Eyth-Allee 100, D-14469 Potsdam, Germany.
| | - Mahnaz Nikaeen
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran; Environment Research Center, Research Institute for Primordial Prevention of Non-Communicable Diseases, Isfahan University of Medical Sciences, Isfahan, Iran.
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Siri Y, Bumyut A, Precha N, Sirikanchana K, Haramoto E, Makkaew P. Multidrug antibiotic resistance in hospital wastewater as a reflection of antibiotic prescription and infection cases. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168453. [PMID: 37956835 DOI: 10.1016/j.scitotenv.2023.168453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/14/2023] [Accepted: 11/07/2023] [Indexed: 11/15/2023]
Abstract
Antimicrobial resistance (AMR) is an escalating issue that can render illnesses more difficult to treat if effective antibiotics become resistant. Many studies have explored antibiotic resistance in bacteria (ARB) in wastewater, comparing results with clinical data to ascertain the public health risk. However, few investigations have linked the prevalence of ARB in hospital wastewater (HWW) with these outcomes. This study aimed to bridge this gap by assessing the prevalence of ARB in HWW and its receiving waters. Among the 144 isolates examined, 24 were obtained from each of the six sites (untreated wastewater, aeration tank, sedimentation tank, effluent after disinfection, upstream canal, and downstream canal). A significant portion (87.5 %) belonged to the Enterobacteriaceae family, with Klebsiella pneumoniae as the predominant species (47.9 %). The antimicrobial sensitivity testing (AST) showed that 57.6 % of the isolates were resistant to amoxicillin/clavulanic acid (AMX), the most prevalent antibiotic used within the studied hospital. The total resistance rate before and after treatment was 27.7 % and 28.0 %, respectively, with an overall multi-drug resistance (MDR) rate of 33.3 %. The multiple antibiotic resistance index (MARI) range varied between 0.0 and 0.9. The outpatient ward's three-day mean bacterial infection cases showed a significant association (Spearman's rho = 0.98) with the MARI in the sedimentation tank. Moreover, a strong correlation (Spearman's rho = 0.88) was found between hospital effluent's MARI and the seven-day mean inpatient ward case. These findings indicate that applying wastewater-based epidemiology (WBE) to hospital wastewater could provide valuable insights into understanding ARB contamination across human domains and water cycles. Future studies, including more comprehensive collection data on symptomatic patients and asymptomatic carriers, will be crucial in fully unravelling the complexities between human health and environmental impacts related to AMR.
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Affiliation(s)
- Yadpiroon Siri
- Environmental, Safety Technology and Health Program, School of Public Health, Walailak University, Thaiburi, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Apirak Bumyut
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; Excellent Center for Dengue and Community Public Health (EC for DACH), Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Nopadol Precha
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; Excellent Center for Dengue and Community Public Health (EC for DACH), Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi 400-8511, Japan
| | - Prasert Makkaew
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; Excellent Center for Dengue and Community Public Health (EC for DACH), Walailak University, Nakhon Si Thammarat 80160, Thailand.
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Yin S, Gao L, Fan X, Gao S, Zhou X, Jin W, He Z, Wang Q. Performance of sewage sludge treatment for the removal of antibiotic resistance genes: Status and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167862. [PMID: 37865259 DOI: 10.1016/j.scitotenv.2023.167862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/23/2023]
Abstract
Wastewater treatment plants (WWTPs) receive wastewater containing antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs), which are predominant contributors to environmental pollution in water and soil. Of these sources, sludge is a more significant contributor than effluent. Knowing how sludge treatment affects the fate of ARGs is vital for managing the risk of these genes in both human and natural environments. This review therefore discusses the sources and transmission of ARGs in the environment and highlights the risks of ARGs in sludge. The effects of co-existing constituents (heavy metals, microplastics, etc.) on sludge and ARGs during treatment are collated to highlight the difficulty of treating sludge with complex constituents in ARGs. The effects of various sludge treatment methods on the abundances of ARGs in sludge and in soil from land application of treated sludge are discussed, pointing out that the choice of sludge treatment method should take into account various potential factors, such as soil and soil biology in subsequent land application. This review offers significant insights and explores the abundances of ARGs throughout the process of sludge treatment and disposal. Unintentional addition of antibiotic residues, heavy metals, microplastics and organic matter in sludge could significantly increase the abundance and reduce the removal efficiency of ARGs during treatment, which undoubtedly adds a barrier to the removal of ARGs from sludge treatment. The complexity of the sludge composition and the diversities of ARGs have led to the fact that no effective sludge treatment method has so far been able to completely eliminate the ecological risk of ARGs. In order to reduce risks resulting by transmission of ARGs, technical and management measures need to be implemented.
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Affiliation(s)
- Shiyu Yin
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China; Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Le Gao
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China; Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Xiumin Fan
- Shenzhen Ecological and Environmental Intelligent Management and Control Center, Shenzhen 518034, China
| | - Shuhong Gao
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China; Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Xu Zhou
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China; Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China.
| | - Wenbiao Jin
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China; Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Zhongqi He
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China; Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
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Castañeda-Barba S, Top EM, Stalder T. Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era. Nat Rev Microbiol 2024; 22:18-32. [PMID: 37430173 DOI: 10.1038/s41579-023-00926-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2023] [Indexed: 07/12/2023]
Abstract
Antimicrobial resistance (AMR) poses a substantial threat to human health. The widespread prevalence of AMR is, in part, due to the horizontal transfer of antibiotic resistance genes (ARGs), typically mediated by plasmids. Many of the plasmid-mediated resistance genes in pathogens originate from environmental, animal or human habitats. Despite evidence that plasmids mobilize ARGs between these habitats, we have a limited understanding of the ecological and evolutionary trajectories that facilitate the emergence of multidrug resistance (MDR) plasmids in clinical pathogens. One Health, a holistic framework, enables exploration of these knowledge gaps. In this Review, we provide an overview of how plasmids drive local and global AMR spread and link different habitats. We explore some of the emerging studies integrating an eco-evolutionary perspective, opening up a discussion about the factors that affect the ecology and evolution of plasmids in complex microbial communities. Specifically, we discuss how the emergence and persistence of MDR plasmids can be affected by varying selective conditions, spatial structure, environmental heterogeneity, temporal variation and coexistence with other members of the microbiome. These factors, along with others yet to be investigated, collectively determine the emergence and transfer of plasmid-mediated AMR within and between habitats at the local and global scale.
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Affiliation(s)
- Salvador Castañeda-Barba
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | - Eva M Top
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
- Institute for Modelling Collaboration and Innovation, University of Idaho, Moscow, ID, USA
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA.
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA.
- Institute for Modelling Collaboration and Innovation, University of Idaho, Moscow, ID, USA.
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40
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Sacramento AG, Fuga B, Fontana H, Cardoso B, Esposito F, Vivas R, Malta JAO, Sellera FP, Lincopan N. Successful expansion of hospital-associated clone of vanA-positive vancomycin-resistant Enterococcus faecalis ST9 to an anthropogenically polluted mangrove in Brazil. MARINE POLLUTION BULLETIN 2024; 198:115844. [PMID: 38056291 DOI: 10.1016/j.marpolbul.2023.115844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/08/2023]
Abstract
Mangrove ecosystems are hotspots of biodiversity, but have been threatened by anthropogenic activities. Vancomycin-resistant enterococci (VRE) are nosocomial bacteria classified as high priority by the World Health Organization (WHO). Herein, we describe the identification and genomic characteristics of a vancomycin-resistant Enterococcus faecalis strain isolated from a highly impacted mangrove ecosystem of the northeastern Brazilian, in 2021. Genomic analysis confirmed the existence of the transposon Tn1546-vanA and clinically relevant antimicrobial resistance genes, such as streptogramins, tetracycline, phenicols, and fluoroquinolones. Virulome analysis identified several genes associated to adherence, immune modulation, biofilm, and exoenzymes production. The UFSEfl strain was assigned to sequence type (ST9), whereas phylogenomic analysis with publicly available genomes from a worldwide confirmed clonal relatedness with a hospital-associated Brazilian clone. Our findings highlight the successful expansion of hospital-associated VRE in a mangrove area and shed light on the need for strengthening genomic surveillance of WHO priority pathogens in these vital ecosystems.
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Affiliation(s)
- Andrey G Sacramento
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
| | - Bruna Fuga
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Brenda Cardoso
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Roberto Vivas
- Microbiology Laboratory, Sergipe Urgent Care Hospital (HUSE), Aracaju, Brazil
| | - Judson A O Malta
- Postgraduate Program in Development and Environment (PRODEMA), Federal University of Sergipe, São Cristóvão, Brazil
| | - Fábio P Sellera
- School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil; Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
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Liu Z, Jin Y, Yu Z, Liu Z, Zhang B, Chi T, Cheng D, Zhu L, Hu B. Vertical migration and dissipation of oxytetracycline induces the recoverable shift in microbial community and antibiotic resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167162. [PMID: 37730066 DOI: 10.1016/j.scitotenv.2023.167162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/29/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
Antibiotic resistance gene (ARG) spread in anthropogenic polluted soils is believed to be accelerated by the incidental inputs of antibiotics via fertilizing and irrigation, and endangering food and human health. However, due to the complex nature of substrates and uncertain microbial responses, the primary drivers of ARG dissemination remain unclear. To address this concern, the effects of antibiotic inputs on soil microbes and antibiotic resistance under simulated natural conditions was investigated in this study. Specifically, four flow-through reactors with gravity flow were established, and the oxytetracycline (OTC) a typical antibiotic in agricultural soils was studied at environmental concentrations (i.e. 0.1, 1 and 10 mg/kg) for 31 days. The vertical distribution and dissipation of OTC were profiled by measuring the residuals in layers over time. Correspondingly, the effects of antibiotic exposure on microbial communities and ARG abundances were studied. The results showed that the average exposure intensity of OTC in different soil layers ranged in 0.03-6.45 mg/kg, and resulted in different dissipation kinetics. In addition, top layer was found to be the main site of OTC reduction, where OTC dissipated at magnitude of 74.0-96.6 %, depending on the initial OTC concentration. OTC migration and dissipation resulted in the shift of community composition to the extent of 0.25-0.33 in terms of Bray-Curtis distance, which partially recovered over time. And the achievement of alternative community compositions was supposed to be largely affected by the microbial interaction. Along with the community changes, a short-term accumulation of resistance genes was detected, while the relative abundance of indicator ARGs, i.e. tetG and mexB, rising up to 10-fold higher than the initial, although eventually decayed. Collective findings of this study indicated that antibiotics at environmental concentrations might trigger extra microbial interactions and thereby reducing the demand for ARGs accumulation. It provided valuable understandings in the risk of antibiotic spillage, especially for the incident exposure at the environmentally relevant concentrations.
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Affiliation(s)
- Zishu Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Yihao Jin
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Zhendi Yu
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Zhengzheng Liu
- Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, China.
| | - Baofeng Zhang
- Hangzhou Ecological and Environmental Monitoring Center, Hangzhou 310007, China.
| | - Taolue Chi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Dongqing Cheng
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310058, China.
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Givens CE, Kolpin DW, Hubbard LE, Meppelink SM, Cwiertny DM, Thompson DA, Lane RF, Wilson MC. Simultaneous stream assessment of antibiotics, bacteria, antibiotic resistant bacteria, and antibiotic resistance genes in an agricultural region of the United States. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166753. [PMID: 37673265 DOI: 10.1016/j.scitotenv.2023.166753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Antimicrobial resistance (AMR) is now recognized as a leading global threat to human health. Nevertheless, there currently is a limited understanding of the environment's role in the spread of AMR and antibiotic resistance genes (ARGs). In 2019, the U.S. Geological Survey conducted the first statewide assessment of antibiotic resistant bacteria (ARB) and ARGs in surface water and bed sediment collected from 34 stream locations across Iowa. Environmental samples were analyzed for a suite of 29 antibiotics and plated on selective media for 15 types of bacteria growth; DNA was extracted from culture growth and used in downstream polymerase chain reaction (PCR) assays for the detection of 24 ARGs. ARGs encoding resistance to antibiotics of clinical importance to human health and disease prevention were prioritized as their presence in stream systems has the potential for environmental significance. Total coliforms, Escherichia coli (E. coli), and staphylococci were nearly ubiquitous in both stream water and stream bed sediment samples, with enterococci present in 97 % of water samples, and Salmonella spp. growth present in 94 % and 67 % of water and bed sediment samples. Bacteria enumerations indicate that high bacteria loads are common in Iowa's streams, with 23 (68 %) streams exceeding state guidelines for primary contact for E. coli in recreational waters and 6 (18 %) streams exceeding the secondary contact advisory level. Although antibiotic-resistant E. coli growth was detected from 40 % of water samples, vancomycin-resistant enterococci (VRE) and penicillinase-resistant Staphylococcus aureus (MRSA) colony growth was detected from nearly all water samples. A total of 14 different ARGs were detected from viable bacteria cells from 30 Iowa streams (88 %, n = 34). Study results provide the first baseline understanding of the prevalence of ARB and ARGs throughout Iowa's waterways and health risk potential for humans, wildlife, and livestock using these waterways for drinking, irrigating, or recreating.
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Affiliation(s)
- Carrie E Givens
- U.S. Geological Survey, 5840 Enterprise Drive, Lansing, MI 48911, USA.
| | - Dana W Kolpin
- U.S. Geological Survey, 400 S. Clinton Street, Iowa City, Iowa 52240, USA
| | - Laura E Hubbard
- U.S. Geological Survey, 1 Gifford Pinchot Drive, Madison, WI 53726, USA
| | | | - David M Cwiertny
- University of Iowa Center for Health Effects of Environmental Contamination, The University of Iowa, 251 North Capitol Street, Chemistry Building - Room W195, Iowa City, Iowa 52242, USA
| | - Darrin A Thompson
- University of Iowa Center for Health Effects of Environmental Contamination, The University of Iowa, 251 North Capitol Street, Chemistry Building - Room W195, Iowa City, Iowa 52242, USA
| | - Rachael F Lane
- U.S. Geological Survey, 1217 Biltmore Drive, Lawrence, Kansas 66049, USA
| | - Michaelah C Wilson
- U.S. Geological Survey, 1217 Biltmore Drive, Lawrence, Kansas 66049, USA
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Takeda-Nishikawa K, Palanichamy R, Miyazato N, Suzuki T. What samples are suitable for monitoring antimicrobial-resistant genes? Using NGS technology, a comparison between eDNA and mrDNA analysis from environmental water. Front Microbiol 2023; 14:954783. [PMID: 38179449 PMCID: PMC10765985 DOI: 10.3389/fmicb.2023.954783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/14/2023] [Indexed: 01/06/2024] Open
Abstract
Introduction The rise in antimicrobial resistance (AMR) that is affecting humans, animals, and the environment, compromises the human immune system and represents a significant threat to public health. Regarding the impact on water sanitation, the risk that antimicrobial-resistant genes (ARGs) and antimicrobial-resistant bacteria in surface water in cities pose to human health remains unclear. To determine the prevalence of AMR in environmental surface water in Japan, we used DNA sequencing techniques on environmental water DNA (eDNA) and the DNA of multidrug-resistant bacteria (mrDNA). Methods The eDNA was extracted from four surface water samples obtained from the Tokyo area and subjected to high- throughput next-generation DNA sequencing using Illumina-derived shotgun metagenome analysis. The sequence data were analyzed using the AmrPlusPlus pipeline and the MEGARes database. Multidrug-resistant bacteria were isolated using a culture-based method from water samples and were screened by antimicrobial susceptibility testing (for tetracycline, ampicillin-sulbactam, amikacin, levofloxacin, imipenem, and clarithromycin). Of the 284 isolates, 22 were identified as multidrug-resistant bacteria. The mrDNA was sequenced using the Oxford nanopore MinION system and analyzed by NanoARG, a web service for detecting and contextualizing ARGs. Results and discussion The results from eDNA and mrDNA revealed that ARGs encoding beta-lactams and multidrug resistance, including multidrug efflux pump genes, were frequently detected in surface water samples. However, mrDNA also revealed many sequence reads from multidrug-resistant bacteria, as well as nonspecific ARGs, whereas eDNA revealed specific ARGs such as pathogenic OXA-type and New Delhi metallo (NDM)-beta-lactamase ARGs. Conclusion To estimate potential AMR pollution, our findings suggested that eDNA is preferable for detecting pathogen ARGs.
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Affiliation(s)
| | - Rajaguru Palanichamy
- Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur, India
| | - Naoki Miyazato
- National Institute of Technology (KOSEN), Gunma College, Maebashi, Japan
| | - Takayoshi Suzuki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Japan
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Liu Y, Smith W, Gebrewold M, Wang X, Simpson SL, Bivins A, Ahmed W. Comparison of concentration and extraction workflows for qPCR quantification of intI1 and vanA in untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166442. [PMID: 37604373 DOI: 10.1016/j.scitotenv.2023.166442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Quantitative polymerase chain reaction (qPCR) measurement of antibiotic resistance genes (ARGs) in untreated municipal wastewater may prove useful in combating the antimicrobial resistance crisis. However, harmonizing and optimizing qPCR-based workflows is essential to facilitate comparisons across studies, and includes achieving highly-effective ARG capture through efficient concentration and extraction procedures. In the current study, combinations of sample volume, membrane types and DNA extraction kits within filtration and centrifugation-based workflows were used to quantify 16S ribosomal RNA (16S rRNA), class 1 integron-integrase gene (intI1) and an ARG encoding resistance to vancomycin (vanA) in untreated wastewater sampled from three wastewater treatment plants (WWTPs). Highly abundant 16S rRNA and intI1 were detected in 100 % of samples from all three WWTPs using both 2 and 20 mL sample volumes, while lower prevalence vanA was only detected when using the 20 mL volume. When filtering 2 mL of wastewater, workflows with 0.20-/0.40-μm polycarbonate (PC) membranes generally yielded greater concentrations of the three targets than workflows with 0.22-/0.45-μm mixed cellulose ester (MCE) membranes. The improved performance was diminished when the sample volume was increased to 20 mL. Consistently greater concentrations of 16S rRNA, intI1 and vanA were yielded by filtration-based workflows using PC membranes combined with a DNeasy PowerWater (DPW) Kit, regardless of the sample volume used, and centrifugation-based workflows with DNeasy Blood & Tissue Kit for 2-mL wastewater extractions. Within the filtration-based workflows, the DPW kit yielded more detection and quantifiable results for less abundant vanA than the DNeasy PowerSoil Pro Kit and FastDNA™ SPIN Kit for Soil. These findings indicate that the performance of qPCR-based workflows for surveillance of ARGs in wastewater varies across targets, sample volumes, concentration methods and extraction kits. Workflows must be carefully considered and validated considering the target ARGs to be monitored.
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Affiliation(s)
- Yawen Liu
- State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China; CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Metasebia Gebrewold
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Xinhong Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | | | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70809, USA
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
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Wheeler NE, Price V, Cunningham-Oakes E, Tsang KK, Nunn JG, Midega JT, Anjum MF, Wade MJ, Feasey NA, Peacock SJ, Jauneikaite E, Baker KS. Innovations in genomic antimicrobial resistance surveillance. THE LANCET. MICROBE 2023; 4:e1063-e1070. [PMID: 37977163 DOI: 10.1016/s2666-5247(23)00285-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/19/2023]
Abstract
Whole-genome sequencing of antimicrobial-resistant pathogens is increasingly being used for antimicrobial resistance (AMR) surveillance, particularly in high-income countries. Innovations in genome sequencing and analysis technologies promise to revolutionise AMR surveillance and epidemiology; however, routine adoption of these technologies is challenging, particularly in low-income and middle-income countries. As part of a wider series of workshops and online consultations, a group of experts in AMR pathogen genomics and computational tool development conducted a situational analysis, identifying the following under-used innovations in genomic AMR surveillance: clinical metagenomics, environmental metagenomics, gene or plasmid tracking, and machine learning. The group recommended developing cost-effective use cases for each approach and mapping data outputs to clinical outcomes of interest to justify additional investment in capacity, training, and staff required to implement these technologies. Harmonisation and standardisation of methods, and the creation of equitable data sharing and governance frameworks, will facilitate successful implementation of these innovations.
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Affiliation(s)
- Nicole E Wheeler
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, Edgbaston, UK
| | - Vivien Price
- Department of Clinical Infection, Immunology and Microbiology, Liverpool Centre for Global Health Research, University of Liverpool, Liverpool, UK
| | - Edward Cunningham-Oakes
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Kara K Tsang
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Jamie G Nunn
- Infectious Disease Challenge Area, Wellcome Trust, London, UK
| | | | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Surrey, UK
| | - Matthew J Wade
- Data Analytics and Surveillance Group, UK Health Security Agency, London, UK; School of Engineering, Newcastle University, Newcastle-upon-Tyne, UK
| | - Nicholas A Feasey
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Chichiri, Blantyre, Malawi
| | | | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Kate S Baker
- Centre for Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK.
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Teixeira AM, Vaz-Moreira I, Calderón-Franco D, Weissbrodt D, Purkrtova S, Gajdos S, Dottorini G, Nielsen PH, Khalifa L, Cytryn E, Bartacek J, Manaia CM. Candidate biomarkers of antibiotic resistance for the monitoring of wastewater and the downstream environment. WATER RESEARCH 2023; 247:120761. [PMID: 37918195 DOI: 10.1016/j.watres.2023.120761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
Urban wastewater treatment plants (UWTPs) are essential for reducing the pollutants load and protecting water bodies. However, wastewater catchment areas and UWTPs emit continuously antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), with recognized impacts on the downstream environments. Recently, the European Commission recommended to monitor antibiotic resistance in UWTPs serving more than 100 000 population equivalents. Antibiotic resistance monitoring in environmental samples can be challenging. The expected complexity of these systems can jeopardize the interpretation capacity regarding, for instance, wastewater treatment efficiency, impacts of environmental contamination, or risks due to human exposure. Simplified monitoring frameworks will be essential for the successful implementation of analytical procedures, data analysis, and data sharing. This study aimed to test a set of biomarkers representative of ARG contamination, selected based on their frequent human association and, simultaneously, rare presence in pristine environments. In addition to the 16S rRNA gene, ten potential biomarkers (intI1, sul1, ermB, ermF, aph(3'')-Ib, qacEΔ1, uidA, mefC, tetX, and crAssphage) were monitored in DNA extracts (n = 116) from raw wastewater, activated sludge, treated wastewater, and surface water (upstream and downstream of UWTPs) samples collected in the Czech Republic, Denmark, Israel, the Netherlands, and Portugal. Each biomarker was sensitive enough to measure decreases (on average by up to 2.5 log-units gene copy/mL) from raw wastewater to surface water, with variations in the same order of magnitude as for the 16S rRNA gene. The use of the 10 biomarkers allowed the typing of water samples whose origin or quality could be predicted in a blind test. The results show that, based on appropriate biomarkers, qPCR can be used for a cost-effective and technically accessible approach to monitoring wastewater and the downstream environment.
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Affiliation(s)
- A Margarida Teixeira
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, Porto 4169-005, Portugal
| | - Ivone Vaz-Moreira
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, Porto 4169-005, Portugal
| | - David Calderón-Franco
- Department of Biotechnology, Environmental Biotechnology Section, Delft University of Technology, van der Maasweg 9, Delft, HZ 2629, the Netherlands
| | - David Weissbrodt
- Department of Biotechnology, Environmental Biotechnology Section, Delft University of Technology, van der Maasweg 9, Delft, HZ 2629, the Netherlands; Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim 7034, Norway
| | - Sabina Purkrtova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, 5 Technická, Prague 166 28, Czech Republic
| | - Stanislav Gajdos
- Department of Water Technology and Environmental Engineering, Faculty of Environmental Technology, University of Chemistry and Technology Prague, 5 Technická, Prague 166 28, Czech Republic
| | - Giulia Dottorini
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg 9220, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg 9220, Denmark
| | - Leron Khalifa
- Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agricultural Research Organization, P.O Box 15159, Rishon Lezion 7528809, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agricultural Research Organization, P.O Box 15159, Rishon Lezion 7528809, Israel
| | - Jan Bartacek
- Department of Water Technology and Environmental Engineering, Faculty of Environmental Technology, University of Chemistry and Technology Prague, 5 Technická, Prague 166 28, Czech Republic
| | - Célia M Manaia
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, Porto 4169-005, Portugal.
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Yalin D, Craddock HA, Assouline S, Ben Mordechay E, Ben-Gal A, Bernstein N, Chaudhry RM, Chefetz B, Fatta-Kassinos D, Gawlik BM, Hamilton KA, Khalifa L, Kisekka I, Klapp I, Korach-Rechtman H, Kurtzman D, Levy GJ, Maffettone R, Malato S, Manaia CM, Manoli K, Moshe OF, Rimelman A, Rizzo L, Sedlak DL, Shnit-Orland M, Shtull-Trauring E, Tarchitzky J, Welch-White V, Williams C, McLain J, Cytryn E. Mitigating risks and maximizing sustainability of treated wastewater reuse for irrigation. WATER RESEARCH X 2023; 21:100203. [PMID: 38098886 PMCID: PMC10719582 DOI: 10.1016/j.wroa.2023.100203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 12/17/2023]
Abstract
Scarcity of freshwater for agriculture has led to increased utilization of treated wastewater (TWW), establishing it as a significant and reliable source of irrigation water. However, years of research indicate that if not managed adequately, TWW may deleteriously affect soil functioning and plant productivity, and pose a hazard to human and environmental health. This review leverages the experience of researchers, stakeholders, and policymakers from Israel, the United-States, and Europe to present a holistic, multidisciplinary perspective on maximizing the benefits from municipal TWW use for irrigation. We specifically draw on the extensive knowledge gained in Israel, a world leader in agricultural TWW implementation. The first two sections of the work set the foundation for understanding current challenges involved with the use of TWW, detailing known and emerging agronomic and environmental issues (such as salinity and phytotoxicity) and public health risks (such as contaminants of emerging concern and pathogens). The work then presents solutions to address these challenges, including technological and agronomic management-based solutions as well as source control policies. The concluding section presents suggestions for the path forward, emphasizing the importance of improving links between research and policy, and better outreach to the public and agricultural practitioners. We use this platform as a call for action, to form a global harmonized data system that will centralize scientific findings on agronomic, environmental and public health effects of TWW irrigation. Insights from such global collaboration will help to mitigate risks, and facilitate more sustainable use of TWW for food production in the future.
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Affiliation(s)
- David Yalin
- A Department of Earth and Planetary Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Hillary A. Craddock
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Shmuel Assouline
- Institute of Soil, Water and Environmental Sciences, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
| | - Evyatar Ben Mordechay
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Alon Ben-Gal
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization (ARO) – The Volcani Institute, Gilat Reseach Center, Israel
| | - Nirit Bernstein
- Institute of Soil, Water and Environmental Sciences, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
| | | | - Benny Chefetz
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Despo Fatta-Kassinos
- Department of Civil and Environmental Engineering, NIREAS-International Water Research Center, University of Cyprus, Nicosia, Cyprus
| | - Bernd M. Gawlik
- Ocean and Water Unit, Joint Research Centre, European Commission, Ispra, Italy
| | - Kerry A. Hamilton
- The School of Sustainable Engineering and the Built Environment and The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA
| | - Leron Khalifa
- Institute of Soil, Water and Environmental Sciences, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
| | - Isaya Kisekka
- Department of Land Air and Water Resources, University of California, Davis, California, USA
| | - Iftach Klapp
- Institute of Agricultural engineering, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
| | | | - Daniel Kurtzman
- Institute of Soil, Water and Environmental Sciences, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
| | - Guy J. Levy
- Institute of Soil, Water and Environmental Sciences, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
| | - Roberta Maffettone
- Ocean and Water Unit, Joint Research Centre, European Commission, Ispra, Italy
| | - Sixto Malato
- CIEMAT-Plataforma Solar de Almería, Ctra. Sen´es km 4, 04200 Tabernas, Almería, Spain
| | - Célia M. Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Kyriakos Manoli
- NIREAS-International Water Research Center, University of Cyprus, Nicosia, Cyprus
| | - Orah F. Moshe
- Department of Soil Conservation, Soil Erosion Research Center, Ministry of Agriculture, Rishon LeZion, Israel
| | - Andrew Rimelman
- PG Environmental. 1113 Washington Avenue, Suite 200. Golden, CO 80401, USA
| | - Luigi Rizzo
- Water Science and Technology (WaSTe) Group, Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - David L. Sedlak
- Department of Civil & Environmental Engineering, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Maya Shnit-Orland
- Extension Service, Ministry of Agriculture and Rural Development, Israel
| | - Eliav Shtull-Trauring
- Institute of Soil, Water and Environmental Sciences, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
| | - Jorge Tarchitzky
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Clinton Williams
- US Arid-Land Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Maricopa, AZ, USA
| | - Jean McLain
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
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48
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Guo B, Wang J, Sathiyan K, Ma X, Lichtfouse E, Huang CH, Sharma VK. Enhanced Oxidation of Antibiotics by Ferrate Mediated with Natural Organic Matter: Role of Phenolic Moieties. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:19033-19042. [PMID: 37384585 PMCID: PMC10862540 DOI: 10.1021/acs.est.3c03165] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023]
Abstract
The increasing presence of antibiotics in water sources threatens public health and ecosystems. Various treatments have been previously applied to degrade antibiotics, yet their efficiency is commonly hindered by the presence of natural organic matter (NOM) in water. On the contrary, we show here that nine types of NOM and NOM model compounds improved the removal of trimethoprim and sulfamethoxazole by ferrate(VI) (FeVIO42-, Fe(VI)) under mild alkaline conditions. This is probably associated with the presence of phenolic moieties in NOMs, as suggested by first-order kinetics using NOM, phenol, and hydroquinone. Electron paramagnetic resonance reveals that NOM radicals are generated within milliseconds in the Fe(VI)-NOM system via single-electron transfer from NOM to Fe(VI) with the formation of Fe(V). The dominance of the Fe(V) reaction with antibiotics resulted in their enhanced removal despite concurrent reactions between Fe(V) and NOM moieties, the radicals, and water. Kinetic modeling considering Fe(V) explains the enhanced kinetics of antibiotics abatement at low phenol concentrations. Experiments with humic and fulvic acids of lake and river waters show similar results, thus supporting the enhanced abatement of antibiotics in real water situations.
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Affiliation(s)
- Binglin Guo
- Department
of Environmental and Occupational Health, School of Public Health, Texas A&M University, College Station, Texas, 77843, USA
- Department
of Civil and Environmental Engineering, Texas A&M University, College
Station, Texas 77843, USA
| | - Junyue Wang
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Krishnamoorthy Sathiyan
- Department
of Environmental and Occupational Health, School of Public Health, Texas A&M University, College Station, Texas, 77843, USA
| | - Xingmao Ma
- Department
of Civil and Environmental Engineering, Texas A&M University, College
Station, Texas 77843, USA
| | - Eric Lichtfouse
- Aix-Marseille
Université, CNRS, IRD, INRAE, College de France, CEREGE, Aix-en-Provence 13100, France
| | - Ching-Hua Huang
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Virender K. Sharma
- Department
of Environmental and Occupational Health, School of Public Health, Texas A&M University, College Station, Texas, 77843, USA
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49
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Mercante LA, Teodoro KBR, dos Santos DM, dos Santos FV, Ballesteros CAS, Ju T, Williams GR, Correa DS. Recent Progress in Stimuli-Responsive Antimicrobial Electrospun Nanofibers. Polymers (Basel) 2023; 15:4299. [PMID: 37959981 PMCID: PMC10647808 DOI: 10.3390/polym15214299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/17/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Electrospun nanofibrous membranes have garnered significant attention in antimicrobial applications, owing to their intricate three-dimensional network that confers an interconnected porous structure, high specific surface area, and tunable physicochemical properties, as well as their notable capacity for loading and sustained release of antimicrobial agents. Tailoring polymer or hybrid-based nanofibrous membranes with stimuli-responsive characteristics further enhances their versatility, enabling them to exhibit broad-spectrum or specific activity against diverse microorganisms. In this review, we elucidate the pivotal advancements achieved in the realm of stimuli-responsive antimicrobial electrospun nanofibers operating by light, temperature, pH, humidity, and electric field, among others. We provide a concise introduction to the strategies employed to design smart electrospun nanofibers with antimicrobial properties. The core section of our review spotlights recent progress in electrospun nanofiber-based systems triggered by single- and multi-stimuli. Within each stimulus category, we explore recent examples of nanofibers based on different polymers and antimicrobial agents. Finally, we delve into the constraints and future directions of stimuli-responsive nanofibrous materials, paving the way for their wider application spectrum and catalyzing progress toward industrial utilization.
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Affiliation(s)
- Luiza A. Mercante
- Institute of Chemistry, Federal University of Bahia (UFBA), Salvador 40170-280, BA, Brazil
| | - Kelcilene B. R. Teodoro
- Nanotechnology National Laboratory for Agriculture (LNNA), Embrapa Instrumentação, São Carlos 13560-970, SP, Brazil; (K.B.R.T.); (D.M.d.S.); (F.V.d.S.)
| | - Danilo M. dos Santos
- Nanotechnology National Laboratory for Agriculture (LNNA), Embrapa Instrumentação, São Carlos 13560-970, SP, Brazil; (K.B.R.T.); (D.M.d.S.); (F.V.d.S.)
| | - Francisco V. dos Santos
- Nanotechnology National Laboratory for Agriculture (LNNA), Embrapa Instrumentação, São Carlos 13560-970, SP, Brazil; (K.B.R.T.); (D.M.d.S.); (F.V.d.S.)
- Department of Materials Engineering, São Carlos School of Engineering, University of São Paulo, São Carlos 13563-120, SP, Brazil
| | - Camilo A. S. Ballesteros
- Bachelor in Natural Sciences and Environmental Education, Pedagogical and Technological University of Colombia (UPTC), Tunja 150003, Colombia;
| | - Tian Ju
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; (T.J.); (G.R.W.)
| | - Gareth R. Williams
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; (T.J.); (G.R.W.)
| | - Daniel S. Correa
- Nanotechnology National Laboratory for Agriculture (LNNA), Embrapa Instrumentação, São Carlos 13560-970, SP, Brazil; (K.B.R.T.); (D.M.d.S.); (F.V.d.S.)
- Department of Materials Engineering, São Carlos School of Engineering, University of São Paulo, São Carlos 13563-120, SP, Brazil
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50
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Siri Y, Precha N, Sirikanchana K, Haramoto E, Makkaew P. Antimicrobial resistance in southeast Asian water environments: A systematic review of current evidence and future research directions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165229. [PMID: 37394072 DOI: 10.1016/j.scitotenv.2023.165229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023]
Abstract
Antimicrobial resistance has been a serious and complex issue for over a decade. Although research on antimicrobial resistance (AMR) has mainly focused on clinical and animal samples as essential for treatment, the AMR situation in aquatic environments may vary and have complicated patterns according to geographical area. Therefore, this study aimed to examine recent literature on the current situation and identify gaps in the AMR research on freshwater, seawater, and wastewater in Southeast Asia. The PubMed, Scopus, and ScienceDirect databases were searched for relevant publications published from January 2013 to June 2023 that focused on antimicrobial resistance bacteria (ARB) and antimicrobial resistance genes (ARGs) among water sources. Based on the inclusion criteria, the final screening included 41 studies, with acceptable agreement assessed using Cohen's inter-examiner kappa equal to 0.866. This review found that 23 out of 41 included studies investigated ARGs and ARB reservoirs in freshwater rather than in seawater and wastewater, and it frequently found that Escherichia coli was a predominant indicator in AMR detection conducted by both phenotypic and genotypic methods. Different ARGs, such as blaTEM, sul1, and tetA genes, were found to be at a high prevalence in wastewater, freshwater, and seawater. Existing evidence highlights the importance of wastewater management and constant water monitoring in preventing AMR dissemination and strengthening effective mitigation strategies. This review may be beneficial for updating current evidence and providing a framework for spreading ARB and ARGs, particularly region-specific water sources. Future AMR research should include samples from various water systems, such as drinking water or seawater, to generate contextually appropriate results. Robust evidence regarding standard detection methods is required for prospective-era work to raise practical policies and alerts for developing microbial source tracking and identifying sources of contamination-specific indicators in aquatic environment markers.
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Affiliation(s)
- Yadpiroon Siri
- Environmental, Safety Technology and Health Program, School of Public Health, Walailak University, Thaiburi, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Nopadol Precha
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi 400-8511, Japan
| | - Prasert Makkaew
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand.
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