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Xue YX, Huang LJ, Wang HY, Peng JJ, Jin MK, Hu SL, Li HB, Xue XM, Zhu YG. Interaction of tetracycline and copper co-intake in inducing antibiotic resistance genes and potential pathogens in mouse gut. ENVIRONMENT INTERNATIONAL 2024; 186:108594. [PMID: 38527398 DOI: 10.1016/j.envint.2024.108594] [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: 01/26/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Abstract
The widespread use of copper and tetracycline as growth promoters in the breeding industry poses a potential threat to environmental health. Nevertheless, to the best of our knowledge, the potential adverse effects of copper and tetracycline on the gut microbiota remain unknown. Herein, mice were fed different concentrations of copper and/or tetracycline for 6 weeks to simulate real life-like exposure in the breeding industry. Following the exposure, antibiotic resistance genes (ARGs), potential pathogens, and other pathogenic factors were analyzed in mouse feces. The co-exposure of copper with tetracycline significantly increased the abundance of ARGs and enriched more potential pathogens in the gut of the co-treated mice. Copper and/or tetracycline exposure increased the abundance of bacteria carrying either ARGs, metal resistance genes, or virulence factors, contributing to the widespread dissemination of potentially harmful genes posing a severe risk to public health. Our study provides insights into the effects of copper and tetracycline exposure on the gut resistome and potential pathogens, and our findings can help reduce the risks associated with antibiotic resistance under the One Health framework.
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Affiliation(s)
- Ying-Xin Xue
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Li-Jie Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Hong-Yu Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Jiangsu Key Laboratory of Vehicle Emissions Control, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Jing-Jing Peng
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Ming-Kang Jin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Shi-Lin Hu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Hong-Bo Li
- State Key Laboratory of Pollution Control and Resource Reuse, Jiangsu Key Laboratory of Vehicle Emissions Control, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Xi-Mei Xue
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
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Alkhanjaf AAM, Sharma S, Sharma M, Kumar R, Arora NK, Kumar B, Umar A, Baskoutas S, Mukherjee TK. Microbial strategies for copper pollution remediation: Mechanistic insights and recent advances. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123588. [PMID: 38401635 DOI: 10.1016/j.envpol.2024.123588] [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: 09/11/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 02/26/2024]
Abstract
Environmental contamination is aninsistent concern affecting human health and the ecosystem. Wastewater, containing heavy metals from industrial activities, significantly contributes to escalating water pollution. These metals can bioaccumulate in food chains, posing health risks even at low concentrations. Copper (Cu), an essential micronutrient, becomes toxic at high levels. Activities like mining and fungicide use have led to Copper contamination in soil, water, and sediment beyond safe levels. Copper widely used in industries, demands restraint of heavy metal ion release into wastewater for ecosystem ultrafiltration, membrane filtration, nanofiltration, and reverse osmosis, combat heavy metal pollution, with emphasis on copper.Physical and chemical approaches are efficient, large-scale feasibility may have drawbackssuch as they are costly, result in the production of sludge. In contrast, bioremediation, microbial intervention offers eco-friendly solutions for copper-contaminated soil. Bacteria and fungi facilitate these bioremediation avenues as cost-effective alternatives. This review article emphasizes on physical, chemical, and biological methods for removal of copper from the wastewater as well asdetailing microorganism's mechanisms to mobilize or immobilize copper in wastewater and soil.
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Affiliation(s)
- Abdulrab Ahmed M Alkhanjaf
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, 11001, Saudi Arabia
| | - Sonu Sharma
- Department of Bio-sciences and Technology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, 133207, Haryana, India
| | - Monu Sharma
- Department of Bio-sciences and Technology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, 133207, Haryana, India
| | - Raman Kumar
- Department of Bio-sciences and Technology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, 133207, Haryana, India.
| | - Naresh Kumar Arora
- Division of Soil and Crop Management, Central Soil Salinity Research Institute, Karnal, 133001, Haryana, India
| | - Brajesh Kumar
- Division of Soil and Crop Management, Central Soil Salinity Research Institute, Karnal, 133001, Haryana, India
| | - Ahmad Umar
- Department of Chemistry, Faculty of Science and Arts, Najran University, Najran, 11001, Saudi Arabia; Department of Materials Science and Engineering, The Ohio State University, Columbus, 43210, OH, USA
| | - Sotirios Baskoutas
- Department of Materials Science, University of Patras, 26500, Patras, Greece
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Haque F, Diba F, Istiaq A, Siddique MA, Mou TJ, Hossain MA, Sultana M. Novel insights into the co-selection of metal-driven antibiotic resistance in bacteria: a study of arsenic and antibiotic co-exposure. Arch Microbiol 2024; 206:194. [PMID: 38538852 DOI: 10.1007/s00203-024-03873-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 04/16/2024]
Abstract
The simultaneous development of antibiotic resistance in bacteria due to metal exposure poses a significant threat to the environment and human health. This study explored how exposure to both arsenic and antibiotics affects the ability of an arsenite oxidizer, Achromobacter xylosoxidans CAW4, to transform arsenite and its antibiotic resistance patterns. The bacterium was isolated from arsenic-contaminated groundwater in the Chandpur district of Bangladesh. We determined the minimum inhibitory concentration (MIC) of arsenite, cefotaxime, and tetracycline for A. xylosoxidans CAW4, demonstrating a multidrug resistance (MDR) trait. Following this determination, we aimed to mimic an environment where A. xylosoxidans CAW4 was exposed to both arsenite and antibiotics. We enabled the strain to grow in sub-MIC concentrations of 1 mM arsenite, 40 µg/mL cefotaxime, and 20 µg/mL tetracycline. The expression dynamics of the arsenite oxidase (aioA) gene in the presence or absence of antibiotics were analyzed. The findings indicated that simultaneous exposure to arsenite and antibiotics adversely affected the bacteria's capacity to metabolize arsenic. However, when arsenite was present in antibiotics-containing media, it promoted bacterial growth. The study observed a global downregulation of the aioA gene in arsenic-antibiotic conditions, indicating the possibility of increased susceptibility through co-resistance across the entire bacterial population of the environment. This study interprets that bacterial arsenic-metabolizing ability can rescue the bacteria from antibiotic stress, further disseminating environmental cross-resistance. Therefore, the co-selection of metal-driven antibiotic resistance in bacteria highlights the need for effective measures to address this emerging threat to human health and the environment.
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Affiliation(s)
- Farhana Haque
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Farzana Diba
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
- Institute of Tissue Banking and Biomaterial Research, Atomic Energy Research Establishment, Savar, Dhaka, 1349, Bangladesh
| | - Arif Istiaq
- Department of Stem Cell Biology, Faculty of Arts and Sciences, Kyushu University, Fukuoka, Japan
| | - Mohammad Anwar Siddique
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
- Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Taslin Jahan Mou
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
- Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
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Wight J, Byrne AS, Tahlan K, Lang AS. Anthropogenic contamination sources drive differences in antimicrobial-resistant Escherichia coli in three urban lakes. Appl Environ Microbiol 2024; 90:e0180923. [PMID: 38349150 PMCID: PMC10952509 DOI: 10.1128/aem.01809-23] [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: 10/13/2023] [Accepted: 01/12/2024] [Indexed: 03/21/2024] Open
Abstract
Antimicrobial resistance (AMR) is an ever-present threat to the treatment of infectious diseases. However, the potential relevance of this phenomenon in environmental reservoirs still raises many questions. Detection of antimicrobial-resistant bacteria in the environment is a critical aspect for understanding the prevalence of resistance outside of clinical settings, as detection in the environment indicates that resistance is likely already widespread. We isolated antimicrobial-resistant Escherichia coli from three urban waterbodies over a 15-month time series, determined their antimicrobial susceptibilities, investigated their population structure, and identified genetic determinants of resistance. We found that E. coli populations at each site were composed of different dominant phylotypes and showed distinct patterns of antimicrobial and multidrug resistance, despite close geographic proximity. Many strains that were genome-sequenced belonged to sequence types of international concern, particularly the ST131 clonal complex. We found widespread resistance to clinically important antimicrobials such as amoxicillin, cefotaxime, and ciprofloxacin, but found that all strains were susceptible to amikacin and the last-line antimicrobials meropenem and fosfomycin. Resistance was most often due to acquirable antimicrobial resistance genes, while chromosomal mutations in gyrA, parC, and parE conferred resistance to quinolones. Whole-genome analysis of a subset of strains further revealed the diversity of the population of E. coli present, with a wide array of AMR and virulence genes identified, many of which were present on the chromosome, including blaCTX-M. Finally, we determined that environmental persistence, transmission between sites, most likely mediated by wild birds, and transfer of mobile genetic elements likely contributed significantly to the patterns observed.IMPORTANCEA One Health perspective is crucial to understand the extent of antimicrobial resistance (AMR) globally, and investigation of AMR in the environment has been increasing in recent years. However, most studies have focused on waterways that are directly polluted by sewage, industrial manufacturing, or agricultural activities. Therefore, there remains a lack of knowledge about more natural, less overtly impacted environments. Through phenotypic and genotypic investigation of AMR in Escherichia coli, this study adds to our understanding of the extent and patterns of resistance in these types of environments, including over a time series, and showed that complex biotic and abiotic factors contribute to the patterns observed. Our study further emphasizes the importance of incorporating the surveillance of microbes in freshwater environments in order to better comprehend potential risks for both human and animal health and how the environment may serve as a sentinel for potential future clinical infections.
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Affiliation(s)
- Jordan Wight
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Alexander S. Byrne
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
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55
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Yan Q, Zhong Z, Li X, Cao Z, Zheng X, Feng G. Characterization of heavy metal, antibiotic pollution, and their resistance genes in paddy with secondary municipal-treated wastewater irrigation. WATER RESEARCH 2024; 252:121208. [PMID: 38309064 DOI: 10.1016/j.watres.2024.121208] [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: 03/02/2023] [Revised: 12/17/2023] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
Secondary municipal-treated wastewater irrigation may introduce residual antibiotics into the agricultural systems contaminated with certain heavy metals, ultimately leading to the coexistence of antibiotics and heavy metals. The coexistence may induce synergistic resistance to both in the microbial community. Here, we investigated the effects of long-term municipal-treated irrigation for rice on the microbiome and resistome. The results showed that the target antibiotics were undetectable in edible grains, and the heavy metal concentrations did not exceed the standard in edible rice grains. Heavy metal resistance genes (MRGs) ruvB and acn antibiotic resistance genes (ARGs) sul1 and sul2 were the dominating resistant genes. The coexistence of antibiotics and heavy metals affected the microbial community and promoted metal and antibiotic resistance. Network analysis revealed that Proteobacteria were the most influential hosts for MRGs, ARGs, and integrons, and co-selection may serve as a potential mechanism for resistance maintenance. MRG czcA and ARG sul1 can be recommended as model genes to study the co-selection of ARGs and MRGs in environments. The obtained results highlight the importance of considering the co-occurrence of heavy metals and antibiotics while developing effective methods to prevent the transmission of ARGs. These findings are critical for assessing the possible human health concerns associated with secondary municipal-treated wastewater irrigation for agriculture and improving the understanding of the coexistence of heavy metals and antibiotics.
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Affiliation(s)
- Qing Yan
- China National Rice Research Institute, Hangzhou 310006, PR China; Rice Product Quality Inspection & Supervision Testing Center, China National Rice Research Institute, Hangzhou 310006, PR China.
| | - Zhengzheng Zhong
- China National Rice Research Institute, Hangzhou 310006, PR China
| | - Xiaoyan Li
- China National Rice Research Institute, Hangzhou 310006, PR China; Rice Product Quality Inspection & Supervision Testing Center, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Zhaoyun Cao
- China National Rice Research Institute, Hangzhou 310006, PR China; Rice Product Quality Inspection & Supervision Testing Center, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Xiaolong Zheng
- China National Rice Research Institute, Hangzhou 310006, PR China; Rice Product Quality Inspection & Supervision Testing Center, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Guozhong Feng
- China National Rice Research Institute, Hangzhou 310006, PR China.
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56
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Vermeire ML, Thiour-Mauprivez C, De Clerck C. Agroecological transition: towards a better understanding of the impact of ecology-based farming practices on soil microbial ecotoxicology. FEMS Microbiol Ecol 2024; 100:fiae031. [PMID: 38479782 PMCID: PMC10994205 DOI: 10.1093/femsec/fiae031] [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: 05/30/2023] [Revised: 12/22/2023] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
Alternative farming systems have developed since the beginning of industrial agriculture. Organic, biodynamic, conservation farming, agroecology and permaculture, all share a grounding in ecological concepts and a belief that farmers should work with nature rather than damage it. As ecology-based agricultures rely greatly on soil organisms to perform the functions necessary for agricultural production, it is thus important to evaluate the performance of these systems through the lens of soil organisms, especially soil microbes. They provide numerous services to plants, including growth promotion, nutrient supply, tolerance to environmental stresses and protection against pathogens. An overwhelming majority of studies confirm that ecology-based agricultures are beneficial for soil microorganisms. However, three practices were identified as posing potential ecotoxicological risks: the recycling of organic waste products, plastic mulching, and pest and disease management with biopesticides. The first two because they can be a source of contaminants; the third because of potential impacts on non-target microorganisms. Consequently, developing strategies to allow a safe recycling of the increasingly growing organic matter stocks produced in cities and factories, and the assessment of the ecotoxicological impact of biopesticides on non-target soil microorganisms, represent two challenges that ecology-based agricultural systems will have to face in the future.
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Affiliation(s)
- Marie-Liesse Vermeire
- CIRAD, UPR Recyclage et Risque, Dakar 18524, Sénégal
- Recyclage et Risque, Univ Montpellier, CIRAD, Montpellier 34398, France
| | - Clémence Thiour-Mauprivez
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie, Dijon 21000, France
| | - Caroline De Clerck
- AgricultureIsLife, Gembloux Agro-Bio Tech, Liege University, 2 Passage des Déportés, 5030 Gembloux, Belgium
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57
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Martiny HM, Pyrounakis N, Petersen TN, Lukjančenko O, Aarestrup FM, Clausen PTLC, Munk P. ARGprofiler-a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets. Bioinformatics 2024; 40:btae086. [PMID: 38377397 PMCID: PMC10918635 DOI: 10.1093/bioinformatics/btae086] [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: 07/10/2023] [Revised: 12/11/2023] [Accepted: 02/19/2024] [Indexed: 02/22/2024] Open
Abstract
MOTIVATION Analyzing metagenomic data can be highly valuable for understanding the function and distribution of antimicrobial resistance genes (ARGs). However, there is a need for standardized and reproducible workflows to ensure the comparability of studies, as the current options involve various tools and reference databases, each designed with a specific purpose in mind. RESULTS In this work, we have created the workflow ARGprofiler to process large amounts of raw sequencing reads for studying the composition, distribution, and function of ARGs. ARGprofiler tackles the challenge of deciding which reference database to use by providing the PanRes database of 14 078 unique ARGs that combines several existing collections into one. Our pipeline is designed to not only produce abundance tables of genes and microbes but also to reconstruct the flanking regions of ARGs with ARGextender. ARGextender is a bioinformatic approach combining KMA and SPAdes to recruit reads for a targeted de novo assembly. While our aim is on ARGs, the pipeline also creates Mash sketches for fast searching and comparisons of sequencing runs. AVAILABILITY AND IMPLEMENTATION The ARGprofiler pipeline is a Snakemake workflow that supports the reuse of metagenomic sequencing data and is easily installable and maintained at https://github.com/genomicepidemiology/ARGprofiler.
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Affiliation(s)
- Hannah-Marie Martiny
- Research Group for Genomic Epidemiology, Technical University of Denmark, Henrik Danms Allé, Bygning 204, Kongens Lyngby 2800, Denmark
| | - Nikiforos Pyrounakis
- Research Group for Genomic Epidemiology, Technical University of Denmark, Henrik Danms Allé, Bygning 204, Kongens Lyngby 2800, Denmark
| | - Thomas N Petersen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Henrik Danms Allé, Bygning 204, Kongens Lyngby 2800, Denmark
| | - Oksana Lukjančenko
- Research Group for Genomic Epidemiology, Technical University of Denmark, Henrik Danms Allé, Bygning 204, Kongens Lyngby 2800, Denmark
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Henrik Danms Allé, Bygning 204, Kongens Lyngby 2800, Denmark
| | - Philip T L C Clausen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Henrik Danms Allé, Bygning 204, Kongens Lyngby 2800, Denmark
| | - Patrick Munk
- Research Group for Genomic Epidemiology, Technical University of Denmark, Henrik Danms Allé, Bygning 204, Kongens Lyngby 2800, Denmark
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Yao T, Ye L, Wang S, Lu J, Li H, Yu G. Effects of cadmium exposure on gut microbiota and antibiotic resistance genes in Haliotis diversicolor abalone. CHEMOSPHERE 2024; 352:141507. [PMID: 38387663 DOI: 10.1016/j.chemosphere.2024.141507] [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: 05/15/2023] [Revised: 12/03/2023] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Heavy metals in soil, water, and industrial production can affect the antibiotic resistance of bacteria. Antibiotic resistance in gut microbiota has been extensively researched. The effects of cadmium (Cd) was investigated on the gut microbiota and antibiotic resistance genes (ARGs) of Haliotis diversicolor, a commercially important abalone species. By exposing H. diversicolor to four concentrations of Cd (0 μg L-1 (control), 6.5 μg L-1 (low), 42.25 μg L-1 (medium), and 274.63 μg L-1 (high)) for 30 and 60 days, 16 types of ARG (aadA-01, aadA-02, cfr, dfrA1, ermB, floR, folA, mecA, sul2, tetB-01, tetC-01, tetD-01, tetG-01, tetM-02, tetQ, vanC-01), and 1213 genus and 27 phylum microbiomes were detected. ARGs can be resistant to aminoglycoside, beta-lactamase, macrolide-lincosamide-streptogramin B, multidrug, florfenicol, macrolide, sulfonamides, tetracyclines, and vancomycin. Cadmium exposure significantly alters the abundance of tetC-01, tetB-01, tetQ, sul2, and aadA-01. About 5% (61) of genus-level microorganisms were significantly affected by Cd exposure. Microbiota alpha and beta diversities in the 60-day 42.25 μg L-1 Cd treatment differed significantly from those in other treatments. In addition, 26 pathogens were detected, and two pathogens (Vibrio and Legionella) were significantly affected by Cd exposure. Significant correlations between pathogens and ARGs increased with increased Cd concentration after 60 days of Cd exposure. Cadmium exposure may cause gut microbiota disturbance in H. diversicolor and increase the likelihood of ARG transfer to pathogens, increasing potential ecological and economic risks.
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Affiliation(s)
- Tuo Yao
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Research Center of Hydrobiology, Jinan University, Guangzhou, China
| | - Lingtong Ye
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Jie Lu
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Gang Yu
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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Stanton IC, Tipper HJ, Chau K, Klümper U, Subirats J, Murray AK. Does Environmental Exposure to Pharmaceutical and Personal Care Product Residues Result in the Selection of Antimicrobial-Resistant Microorganisms, and is this Important in Terms of Human Health Outcomes? ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024; 43:623-636. [PMID: 36416260 DOI: 10.1002/etc.5498] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/14/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The environment plays a critical role in the development, dissemination, and transmission of antimicrobial resistance (AMR). Pharmaceuticals and personal care products (PPCPs) enter the environment through direct application to the environment and through anthropogenic pollution. Although there is a growing body of evidence defining minimal selective concentrations (MSCs) of antibiotics and the role antibiotics play in horizontal gene transfer (HGT), there is limited evidence on the role of non-antibiotic PPCPs. Existing data show associations with the development of resistance or effects on bacterial growth rather than calculating selective endpoints. Research has focused on laboratory-based systems rather than in situ experiments, although PPCP concentrations found throughout wastewater, natural water, and soil environments are often within the range of laboratory-derived MSCs and at concentrations shown to promote HGT. Increased selection and HGT of AMR by PPCPs will result in an increase in total AMR abundance in the environment, increasing the risk of exposure and potential transmission of environmental AMR to humans. There is some evidence to suggest that humans can acquire resistance from environmental settings, with water environments being the most frequently studied. However, because this is currently limited, we recommend that more evidence be gathered to understand the risk the environment plays in regard to human health. In addition, we recommend that future research efforts focus on MSC-based experiments for non-antibiotic PPCPS, particularly in situ, and investigate the effect of PPCP mixtures on AMR. Environ Toxicol Chem 2024;43:623-636. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
| | | | - Kevin Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Uli Klümper
- Institute of Hydrobiology, Technische Universitӓt Dresden, Dresden, Germany
| | - Jessica Subirats
- Institute of Environmental Assessment and Water Research, Spanish Council for Scientific Research (IDAEA-CSIC), Barcelona, Spain
| | - Aimee K Murray
- College of Medicine and Health, University of Exeter, Cornwall, UK
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60
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Maskrey BH, Dean K, Morrell N, Younger A, Turner AD, Katsiadaki I. Seasonal profile of common pharmaceuticals in edible bivalve molluscs. MARINE POLLUTION BULLETIN 2024; 200:116128. [PMID: 38377862 DOI: 10.1016/j.marpolbul.2024.116128] [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: 10/10/2023] [Revised: 01/31/2024] [Accepted: 02/03/2024] [Indexed: 02/22/2024]
Abstract
Pharmaceuticals are recognised as environmental contaminants of emerging concern (CECs) due to their increasing presence in the aquatic environment, along with high bioactivity linked to their therapeutic use. Therefore, information on environmental levels is urgently required. This study examined the presence of a range of common pharmaceuticals in oysters and mussels intended for human consumption from England and Wales using stable isotope dilution tandem mass spectrometry. A range of compounds were detected in bivalve tissue, with the Selective Serotonin Reuptake Inhibitor antidepressant sertraline being most abundant, reaching a maximum concentration of 22.1 ng/g wet weight shellfish tissue. Levels of all pharmaceuticals showed seasonal and geographical patterns. A dietary risk assessment revealed that the levels of pharmaceuticals identified in bivalve molluscs represent a clear hazard, but not a risk for the consumer. This study highlights the requirement for further monitoring of the presence of pharmaceuticals and other CECs in bivalve molluscs.
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Affiliation(s)
- Benjamin H Maskrey
- Centre for Environment Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom.
| | - Karl Dean
- Centre for Environment Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom
| | - Nadine Morrell
- Centre for Environment Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom
| | - Andrew Younger
- Centre for Environment Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom
| | - Andrew D Turner
- Centre for Environment Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom
| | - Ioanna Katsiadaki
- Centre for Environment Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom
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Qi W, Jonker MJ, Katsavelis D, de Leeuw W, Wortel M, Ter Kuile BH. The Effect of the Stringent Response and Oxidative Stress Response on Fitness Costs of De Novo Acquisition of Antibiotic Resistance. Int J Mol Sci 2024; 25:2582. [PMID: 38473832 DOI: 10.3390/ijms25052582] [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: 12/20/2023] [Revised: 02/12/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Resistance evolution during exposure to non-lethal levels of antibiotics is influenced by various stress responses of bacteria which are known to affect growth rate. Here, we aim to disentangle how the interplay between resistance development and associated fitness costs is affected by stress responses. We performed de novo resistance evolution of wild-type strains and single-gene knockout strains in stress response pathways using four different antibiotics. Throughout resistance development, the increase in minimum inhibitory concentration (MIC) is accompanied by a gradual decrease in growth rate, most pronounced in amoxicillin or kanamycin. By measuring biomass yield on glucose and whole-genome sequences at intermediate and final time points, we identified two patterns of how the stress responses affect the correlation between MIC and growth rate. First, single-gene knockout E. coli strains associated with reactive oxygen species (ROS) acquire resistance faster, and mutations related to antibiotic permeability and pumping out occur earlier. This increases the metabolic burden of resistant bacteria. Second, the ΔrelA knockout strain, which has reduced (p)ppGpp synthesis, is restricted in its stringent response, leading to diminished growth rates. The ROS-related mutagenesis and the stringent response increase metabolic burdens during resistance development, causing lower growth rates and higher fitness costs.
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Affiliation(s)
- Wenxi Qi
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Martijs J Jonker
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Drosos Katsavelis
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Wim de Leeuw
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Meike Wortel
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Benno H Ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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Yu Y, Zhang Q, Kang J, Xu N, Zhang Z, Deng Y, Gillings M, Lu T, Qian H. Effects of organic fertilizers on plant growth and the rhizosphere microbiome. Appl Environ Microbiol 2024; 90:e0171923. [PMID: 38193672 PMCID: PMC10880660 DOI: 10.1128/aem.01719-23] [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: 09/27/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Application of organic fertilizers is an important strategy for sustainable agriculture. The biological source of organic fertilizers determines their specific functional characteristics, but few studies have systematically examined these functions or assessed their health risk to soil ecology. To fill this gap, we analyzed 16S rRNA gene amplicon sequencing data from 637 soil samples amended with plant- and animal-derived organic fertilizers (hereafter plant fertilizers and animal fertilizers). Results showed that animal fertilizers increased the diversity of soil microbiome, while plant fertilizers maintained the stability of soil microbial community. Microcosm experiments verified that plant fertilizers were beneficial to plant root development and increased carbon cycle pathways, while animal fertilizers enriched nitrogen cycle pathways. Compared with animal fertilizers, plant fertilizers harbored a lower abundance of risk factors such as antibiotic resistance genes and viruses. Consequently, plant fertilizers might be more suitable for long-term application in agriculture. This work provides a guide for organic fertilizer selection from the perspective of soil microecology and promotes sustainable development of organic agriculture.IMPORTANCEThis study provides valuable guidance for use of organic fertilizers in agricultural production from the perspective of the microbiome and ecological risk.
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Affiliation(s)
- Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Jian Kang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Yu Deng
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic Biology, Faculty of Science and Engineering, Macquarie University, New South Wales, Australia
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, China
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Pan Z, Wang W, Chen J, Chen Z, Avellán-Llaguno RD, Xu W, Duan Y, Liu B, Huang Q. Temporal dynamics of microbial composition and antibiotic resistome in fermentation bed culture pig farms across various ages. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168728. [PMID: 37992830 DOI: 10.1016/j.scitotenv.2023.168728] [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: 09/26/2023] [Revised: 11/18/2023] [Accepted: 11/18/2023] [Indexed: 11/24/2023]
Abstract
The discharge from pig farms presents significant challenges to the environment and human health, specifically regarding the dissemination of antimicrobial resistance (AMR). Fermentation bed culture has emerged as an increasingly popular and environmentally friendly pig farming model in China, as it minimizes the release of harmful substances into the environment. However, there remains a limited understanding of the occurrence and dynamics of microbiome and antibiotic resistome in fermentation bed culture. Herein, we collected fermentation bed materials (FBM) from four fermentation bed culture pig farms with varying service ages and investigated their bacterial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metal resistance genes (MRGs) and potential antibiotic-resistant bacterial hosts through metagenomics. Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota were identified as the dominant phyla present in the FBM. In total, we detected 258 unique ARGs in the FBM samples, with 79 core ARGs shared by all FBM samples, accounting for 95 % of the total ARG abundance. Our results revealed significant variations in microbial communities and ARG profiles across varying service ages of FBM. Compared to long-term FBW, short-term FBM exhibited higher numbers and abundances of ARGs, MRGs and MGEs, along with higher levels of potential bacterial pathogens and high-risk ARGs. Further analysis of metagenome-assembled genome (MAG) indicated that the putative hosts of ARGs primarily belonged to Pseudomonadota, Actinomycetota and Bacillota. Alarmingly, among the 80 recovered ARG-carrying MAGs, 23 MAGs encoded multi-resistance, including clinically significant species that require urgent attention. Overall, this study provided valuable insights into the temporal patterns of antibiotic resistome and bacterial communities within FBM, enhancing our understanding of FBM in pig farming. The findings could potentially contribute to the development of effective strategies for evaluating and regulating fermentation bed culture practices in pig farming.
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Affiliation(s)
- Zhizhen Pan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Weiyi Wang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Institute of Life Sciences and Green Development, College of Life Sciences, Hebei University, Hebei 071002, China
| | - Jingyu Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Zheng Chen
- Institue of Plant Protection, Fujian Academy of Agriculture Sciences, Fuzhou 350003, China
| | - Ricardo David Avellán-Llaguno
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Wenjuan Xu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yifang Duan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Bo Liu
- Fujian Academy of Agriculture Sciences, Fuzhou 350003, China
| | - Qiansheng Huang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Li YJ, Yuan Y, Tan WB, Xi BD, Wang H, Hui KL, Chen JB, Zhang YF, Wang LF, Li RF. Antibiotic resistance genes and heavy metals in landfill: A review. JOURNAL OF HAZARDOUS MATERIALS 2024; 464:132395. [PMID: 37976849 DOI: 10.1016/j.jhazmat.2023.132395] [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: 07/05/2023] [Revised: 08/07/2023] [Accepted: 08/23/2023] [Indexed: 11/19/2023]
Abstract
Landfill is reservoir containing antibiotic resistance genes (ARGs) that pose a threat to human life and health. Heavy metals impose lasting effects on ARGs. This review investigated and analyzed the distribution, composition, and abundance of heavy metals and ARGs in landfill. The abundance ranges of ARGs detected in refuse and leachate were similar. The composition of ARG varied with sampling depth in refuse. ARG in leachate varies with the distribution of ARG in the refuse. The ARG of sulI was associated with 11 metals (Co, Pb, Mn, Zn, Cu, Cr, Ni, Sb, As, Cd, and Al). The effects of the total metal concentration on ARG abundance were masked by many factors. Low heavy metal concentrations showed positive effects on ARG diffusion; conversely, high heavy metal concentrations showed negative effects. Organic matter had a selective pressure effect on microorganisms and could provide energy for the diffusion of ARGs. Complexes of heavy metals and organic matter were common in landfill. Therefore, the hypothesis was proposed that organic matter and heavy metals have combined effects on the horizontal gene transfer (HGT) of ARGs during landfill stabilization. This work provides a new basis to better understand the HGT of ARGs in landfill.
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Affiliation(s)
- Yan-Jiao Li
- School of Materials Science and engineering, Dalian Jiaotong University, Dalian 116021, China; State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Ying Yuan
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Wen-Bing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Bei-Dou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Hui Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Kun-Long Hui
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jia-Bao Chen
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yi-Fan Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Lian-Feng Wang
- School of Materials Science and engineering, Dalian Jiaotong University, Dalian 116021, China
| | - Ren-Fei Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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Zhang M, Xiong Y, Sun H, Xiao T, Xiao E, Sun X, Li B, Sun W. Selective pressure of arsenic and antimony co-contamination on microbial community in alkaline sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 464:132948. [PMID: 37984136 DOI: 10.1016/j.jhazmat.2023.132948] [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: 09/03/2023] [Revised: 10/27/2023] [Accepted: 11/05/2023] [Indexed: 11/22/2023]
Abstract
Although response of microbial community to arsenic (As) and antimony (Sb) co-contamination has been investigated in neutral and acidic environments, little is known in alkaline environment. Herein, the microbial response and survival strategies under the stress of As and Sb co-contamination were determined in the alkaline sediments. Elevated concentrations of As (13700 ± 5012 mg/kg) and Sb (10222 ± 1619 mg/kg) were introduced into the alkaline sediments by the mine drainage, which was partially adopted in the aquatic environment and resulted in a relatively lower contamination (As, 6633 ± 1707 mg/kg; Sb, 6108 ± 1095 mg/kg) in the downstream sediments. The microbial richness was significantly damaged and the microbial compositions were dramatically shifted by the As and Sb co-contamination. Metagenomic analysis shed light on the survival strategies of the microbes under the pressure of As and Sb co-contamination including metal oxidation coupled with denitrification, metal reduction, and metal resistance. The representative microbes were revealed in the sediments with higher (Halomonas) and lower (Thiobacillus, Hydrogenophaga and Flavihumibacter) As and Sb concentration, respectively. In addition, antibiotic resistance genes were found to co-occur with metal resistance genes in the assembled bins. These findings might provide theoretical guidance for bioremediation of As and Sb co-contamination in alkaline environment.
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Affiliation(s)
- Miaomiao Zhang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yiqun Xiong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, China; Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Huicai Sun
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Tangfu Xiao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Enzong Xiao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, China; Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, China; Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
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66
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Ahmed N, Azab M, Enany S, Hanora A. Draft genome sequence of novel Candidatus Ornithobacterium hominis carrying antimicrobial resistance genes in Egypt. BMC Microbiol 2024; 24:47. [PMID: 38302869 PMCID: PMC10835994 DOI: 10.1186/s12866-023-03172-6] [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: 09/06/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Candidatus Ornithobacterium hominis (O. hominis), which was identified in nasopharyngeal swabs from Egypt, has been associated with respiratory disorders in humans. O. hominis, a recently identified member of the Flavobacteriaceae family, belongs to the largest family within the Bacteroidetes phylum. This family includes hundreds of species and 90 genera, including major human pathogens such as Capnocytophaga canimorsus and Elizabethkingia meningoseptica. Herein, we presented two draft genome assemblies of O. hominis that were extracted from metagenomic data using the Illumina sequencing method. The alignment of reads against the O. hominis genome was accomplished using BLASTN, and the reads with significant hits were extracted using Seqtk and assembled using SPAdes. The primary goal of this study was to obtain a more profound understanding of the genomic landscape of O. hominis, with an emphasis on identifying the associated virulence, antimicrobial genes, and distinct defense mechanisms to shed light on the potential role of O. hominis in human respiratory infections. RESULTS The genome size was estimated to be 1.84 Mb, including 1,931,660 base pairs (bp), with 1,837 predicted coding regions and a G+C content of 35.62%. Genes encoding gliding motility, antibiotic resistance (20 genes), and the toxA gene were all included in the genome assembly. Gliding motility lipoproteins (GldD, GldJ, GldN, and GldH) and the gliding motility-associated ABC transporter substrate-binding protein, which acts as a crucial virulence mechanism in Flavobacterium species, were identified. The genome contained unique genes encoding proteins, such as the ParE1 toxin that defend against the actions of quinolone and other antibiotics. The cobalt-zinc-cadmium resistance gene encoding the protein CzcB, which is necessary for metal resistance, urease regulation, and colonization, was also detected. Several multidrug resistance genes encoding proteins were identified, such as MexB, MdtK, YheI, and VanC. CONCLUSION Our study focused on identifying virulence factors, and antimicrobial resistance genes present in the core genome of O. hominis. These findings provide valuable insights into the potential pathogenicity and antibiotic susceptibility of O. hominis.
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Affiliation(s)
- Nada Ahmed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Marwa Azab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Shymaa Enany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt.
- Biomedical Research Department, Armed Force College of Medicine, Cairo, Egypt.
| | - Amro Hanora
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt.
- Department of Microbiology & Immunology, Faculty of Pharmacy, King Salman International University, Ras Sudr, Egypt.
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Banchi E, Corre E, Del Negro P, Celussi M, Malfatti F. Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:126-142. [PMID: 38433960 PMCID: PMC10902248 DOI: 10.1007/s42995-023-00192-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 09/05/2023] [Indexed: 03/05/2024]
Abstract
Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from 'omics' approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g., C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00192-z.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Erwan Corre
- FR2424, Station Biologique de Roscoff, Plateforme ABiMS (Analysis and Bioinformatics for Marine Science), Sorbonne Université CNRS, 29680 Roscoff, France
| | - Paola Del Negro
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Francesca Malfatti
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
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Chai J, Zhuang Y, Cui K, Bi Y, Zhang N. Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids. MICROBIOME 2024; 12:14. [PMID: 38254181 PMCID: PMC10801991 DOI: 10.1186/s40168-023-01733-5] [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: 01/23/2022] [Accepted: 11/28/2023] [Indexed: 01/24/2024]
Abstract
BACKGROUND The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of antibiotic resistance. Although it has been reported that the rumen microbiome of ruminants may be a reservoir of ARGs, the factors affecting the temporal dynamics of the rumen resistome are still unclear. Here, we collected rumen content samples of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days of age, analyzed their microbiome and resistome profiles using metagenomics, and assessed the temporal dynamics of the rumen resistome in goats at the early stage of life under a conventional feeding system. RESULTS In our results, the rumen resistome of goat kids contained ARGs to 41 classes, and the richness of ARGs decreased with age. Four antibiotic compound types of ARGs, including drugs, biocides, metals, and multi-compounds, were found during milk feeding, while only drug types of ARGs were observed after supplementation with starter feed. The specific ARGs for each age and their temporal dynamics were characterized, and the network inference model revealed that the interactions among ARGs were related to age. A strong correlation between the profiles of rumen resistome and microbiome was found using Procrustes analysis. Ruminal Escherichia coli within Proteobacteria phylum was the main carrier of ARGs in goats consuming colostrum, while Prevotella ruminicola and Fibrobacter succinogenes associated with cellulose degradation were the carriers of ARGs after starter supplementation. Milk consumption was likely a source of rumen ARGs, and the changes in the rumen resistome with age were correlated with the microbiome modulation by starter supplementation. CONCLUSIONS Our data revealed that the temporal dynamics of the rumen resistome are associated with the microbiome, and the reservoir of ARGs in the rumen during early life is likely related to age and diet. It may be a feasible strategy to reduce the rumen and its downstream dissemination of ARGs in ruminants through early-life dietary intervention. Video Abstract.
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Affiliation(s)
- Jianmin Chai
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Yimin Zhuang
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Kai Cui
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yanliang Bi
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
| | - Naifeng Zhang
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, 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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Li K, Zhu Y, Shi X, Yan M, Li J, Zhang W, Shao Y, Shao Y. Effects of Zn and oxytetracycline on mobile genetic elements, antibiotic resistance genes, and microbial community evolution in soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:122609. [PMID: 37742856 DOI: 10.1016/j.envpol.2023.122609] [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: 08/12/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 09/26/2023]
Abstract
Antibiotics and heavy metals added to livestock and poultry feed are excreted in manure, which is added to agricultural soil and causes severe pollution. However, the effects of oxytetracycline (OTC) and zinc (Zn), which are present at relatively high levels in feed additives, on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial communities have not been comprehensively studied. This study evaluated the effects of OTC and Zn on environmental factors, microorganisms, MGEs, and ARGs. The expression of MGEs in soil was stimulated by adding Zn at concentrations of 500 and 1000 mg/kg or OTC at concentrations of 30 and 100 mg/kg; however, the addition of their combination hindered the expression of MGEs in soil. The abundance of total MGEs and ARGs tended to decrease with increasing concentrations of Zn and OTC and the number of incubation days. Low and high OTC concentrations strongly inhibited sul and tet resistance genes, respectively. Network analysis showed that changes in the population of Firmicutes and Proteobacteria had the greatest impact on ARG abundance. Redundancy analysis revealed that MGEs, particularly intI2, facilitated the transfer and spread of ARGs and had the greatest impact on changes in ARG abundance. These findings provide reference values for the prevention and resolution of ecological and environmental risks posed by the presence of Zn and OTC in organic manure soil.
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Affiliation(s)
- Ke Li
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Ying Zhu
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Xinhua Shi
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Maolu Yan
- Shandong Ecological Home Environmental Protection Co., LTD, Jinan, 250000, China
| | - Jing Li
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Weiyi Zhang
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Yingying Shao
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Yanqiu Shao
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China.
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71
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Zhang H, Xu Y, Shen T, Jia X, Xu Y, Shi T, Pan D, Hua R, Wu X. Chicken feedlot revisited: Co-dispersal of antibiotic and metal resistome under banning in-feed veterinary antibiotics. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:122932. [PMID: 37979651 DOI: 10.1016/j.envpol.2023.122932] [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: 08/07/2023] [Revised: 11/04/2023] [Accepted: 11/11/2023] [Indexed: 11/20/2023]
Abstract
Intensive livestock farming has been implicated as a notorious hotspot for antibiotic resistance genes (ARGs) due to the excessive or inappropriate use of in-feed antibiotics over the past few decades. Since China implemented a ban on the use of antibiotics in animal feed since 2020, the dissemination of ARGs in the vicinity of feedlots has remained unclear. This study presents a case study that aims to investigate the dispersal of antibiotics and ARGs from a chicken feedlot (established in 2020) to the adjacent aquatic and soil environments. Comparing the sample collected from upstream area, the water and sediment samples from midstream and downstream areas showed an increase in total antibiotic residues and metal content (Cu and Zn) by 4.2-5.3 fold and 1.3-22.6 fold, respectively. The downstream water samples exhibited a 2.49-2.93-fold increase in the abundance of ARGs and a 1.48-1.75-fold increase in the abundance of metal resistance genes (MRGs). The results of Pearson correlation and metagenome-assembled genome revealed a tendency for the co-occurrence of ARGs and MRGs. The dissemination of ARGs and MRGs is primarily driven by tetracycline, tylosin, Cu, and, Mn, with mobile genetic elements playing a more significant role than bacterial communities. These findings shed light on the overlooked co-dispersal pattern of ARGs and MRGs in the environment surrounding feedlots, particularly in the context of banning in-feed veterinary antibiotics.
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Affiliation(s)
- Houpu Zhang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Yingqian Xu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Tiantian Shen
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Xinyu Jia
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Yuer Xu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Taozhong Shi
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Dandan Pan
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Rimao Hua
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China
| | - Xiangwei Wu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, PR China.
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72
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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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73
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Ruhluel D, Fisher L, Barton TE, Leighton H, Kumar S, Amores Morillo P, O’Brien S, Fothergill JL, Neill DR. Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments. THE ISME JOURNAL 2024; 18:wrae065. [PMID: 38647527 PMCID: PMC11102083 DOI: 10.1093/ismejo/wrae065] [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: 12/09/2023] [Revised: 03/08/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
Pseudomonas aeruginosa is a cause of chronic respiratory tract infections in people with cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease. Prolonged infection allows the accumulation of mutations and horizontal gene transfer, increasing the likelihood of adaptive phenotypic traits. Adaptation is proposed to arise first in bacterial populations colonizing upper airway environments. Here, we model this process using an experimental evolution approach. Pseudomonas aeruginosa PAO1, which is not airway adapted, was serially passaged, separately, in media chemically reflective of upper or lower airway environments. To explore whether the CF environment selects for unique traits, we separately passaged PAO1 in airway-mimicking media with or without CF-specific factors. Our findings demonstrated that all airway environments-sinus and lungs, under CF and non-CF conditions-selected for loss of twitching motility, increased resistance to multiple antibiotic classes, and a hyper-biofilm phenotype. These traits conferred increased airway colonization potential in an in vivo model. CF-like conditions exerted stronger selective pressures, leading to emergence of more pronounced phenotypes. Loss of twitching was associated with mutations in type IV pili genes. Type IV pili mediate surface attachment, twitching, and induction of cAMP signalling. We additionally identified multiple evolutionary routes to increased biofilm formation involving regulation of cyclic-di-GMP signalling. These included the loss of function mutations in bifA and dipA phosphodiesterase genes and activating mutations in the siaA phosphatase. These data highlight that airway environments select for traits associated with sessile lifestyles and suggest upper airway niches support emergence of phenotypes that promote establishment of lung infection.
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Affiliation(s)
- Dilem Ruhluel
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, United Kingdom
| | - Lewis Fisher
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Thomas E Barton
- Division of Molecular Microbiology, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Hollie Leighton
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, United Kingdom
| | - Sumit Kumar
- Division of Molecular Microbiology, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Paula Amores Morillo
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, United Kingdom
| | - Siobhan O’Brien
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, 2, Ireland
| | - Joanne L Fothergill
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, United Kingdom
| | - Daniel R Neill
- Division of Molecular Microbiology, University of Dundee, Dow Street, Dundee, United Kingdom
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74
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Cui Y, Gao J, Zeng L, Guo Y, Xu H, Zhao M. Different fates of extracellular and intracellular antibiotic resistance genes in flocs, granular and biofilm nitrification systems under the stress of acetaminophen. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132675. [PMID: 37806259 DOI: 10.1016/j.jhazmat.2023.132675] [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: 08/08/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 10/10/2023]
Abstract
The spread of antibiotic resistance genes (ARGs), including intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs), has become a global problem that cannot be ignored. This study clarified the fates of e-ARGs and i-ARGs in floc sludge reactor (FS), granular sludge reactor (GS) and biofilm reactor (BF) under the stress of acetaminophen (APAP). The results showed that the risk of ARGs transmission, especially for e-ARGs, in FS and BF could increase with the increasing times of APAP treatment, except for that in GS. The fates of i-ARGs in three different systems were similar, which were mainly clustered as the efflux pumps mechanism. The secretion and disintegration of extracellular polymeric substances mainly affected the fates of e-ARGs. In the three systems, the complexity of network relationships between ARGs and microbial communities was FS, GS and BF. Partial least-squares path model analysis indicated that bacterial community directly contributed to the variations of e-ARGs and i-ARGs under APAP treatment in the three systems, playing a leading role. And i-ARGs and protein secondary structure showed direct effects on e-ARGs. This study indicated that e-ARGs in complex systems were more susceptible to be influenced, which should be paid more attention to prevent further propagation of ARGs.
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Affiliation(s)
- Yingchao Cui
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Jingfeng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China.
| | - Liqin Zeng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yi Guo
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Hongxin Xu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Mingyan Zhao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
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75
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Kopf A, Bunk B, Riedel T, Schröttner P. The zoonotic pathogen Wohlfahrtiimonas chitiniclastica - current findings from a clinical and genomic perspective. BMC Microbiol 2024; 24:3. [PMID: 38172653 PMCID: PMC10763324 DOI: 10.1186/s12866-023-03139-7] [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: 08/01/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
The zoonotic pathogen Wohlfahrtiimonas chitiniclastica can cause several diseases in humans, including sepsis and bacteremia. Although the pathogenesis is not fully understood, the bacterium is thought to enter traumatic skin lesions via fly larvae, resulting in severe myiasis and/or wound contamination. Infections are typically associated with, but not limited to, infestation of an open wound by fly larvae, poor sanitary conditions, cardiovascular disease, substance abuse, and osteomyelitis. W. chitiniclastica is generally sensitive to a broad spectrum of antibiotics with the exception of fosfomycin. However, increasing drug resistance has been observed and its development should be monitored with caution. In this review, we summarize the currently available knowledge and evaluate it from both a clinical and a genomic perspective.
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Affiliation(s)
- Anna Kopf
- Clinic for Cardiology, Sana Heart Center, Leipziger Str. 50, 03048, Cottbus, Germany
- 2nd Medical Clinic for Hematology, Oncology, Pneumology and Nephrology, Carl-Thiem Hospital Cottbus gGmbH, Cottbus, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Percy Schröttner
- Institute for Medical Microbiology and Virology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
- Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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76
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Bodilis J, Simenel O, Michalet S, Brothier E, Meyer T, Favre-Bonté S, Nazaret S. HME, NFE, and HAE-1 efflux pumps in Gram-negative bacteria: a comprehensive phylogenetic and ecological approach. ISME COMMUNICATIONS 2024; 4:ycad018. [PMID: 38371394 PMCID: PMC10872679 DOI: 10.1093/ismeco/ycad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/15/2023] [Accepted: 12/26/2023] [Indexed: 02/20/2024]
Abstract
The three primary resistance-nodulation-cell division (RND) efflux pump families (heavy metal efflux [HME], nodulation factor exporter [NFE], and hydrophobe/amphiphile efflux-1 [HAE-1]) are almost exclusively found in Gram-negative bacteria and play a major role in resistance against metals and bacterial biocides, including antibiotics. Despite their significant societal interest, their evolutionary history and environmental functions are poorly understood. Here, we conducted a comprehensive phylogenetic and ecological study of the RND permease, the subunit responsible for the substrate specificity of these efflux pumps. From 920 representative genomes of Gram-negative bacteria, we identified 6205 genes encoding RND permeases with an average of 6.7 genes per genome. The HME family, which is involved in metal resistance, corresponds to a single clade (21.8% of all RND pumps), but the HAE-1 and NFE families had overlapping distributions among clades. We propose to restrict the HAE-1 family to two phylogenetic sister clades, representing 41.8% of all RND pumps and grouping most of the RND pumps involved in multidrug resistance. Metadata associated with genomes, analyses of previously published metagenomes, and quantitative Polymerase Chain Reaction (qPCR) analyses confirmed a significant increase in genes encoding HME permeases in metal-contaminated environments. Interestingly, and possibly related to their role in root colonization, genes encoding HAE-1 permeases were particularly abundant in the rhizosphere. In addition, we found that the genes encoding these HAE-1 permeases are significantly less abundant in marine environments, whereas permeases of a new proposed HAE-4 family are predominant in the genomes of marine strains. These findings emphasize the critical role of the RND pumps in bacterial resistance and adaptation to diverse ecological niches.
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Affiliation(s)
- Josselin Bodilis
- Université Rouen Normandie, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, Rouen Institute for Research and Innovation in Biomedicine, Mont-Saint-Aignan F-76821, France
- Université Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Ecologie Microbienne, Villeurbanne F-69622, France
| | - Olwen Simenel
- Université Rouen Normandie, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, Rouen Institute for Research and Innovation in Biomedicine, Mont-Saint-Aignan F-76821, France
- Université Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Ecologie Microbienne, Villeurbanne F-69622, France
- Université Rouen Normandie, LMSM EA4312, Evreux F-27000, France
| | - Serge Michalet
- Université Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Ecologie Microbienne, Villeurbanne F-69622, France
| | - Elisabeth Brothier
- Université Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Ecologie Microbienne, Villeurbanne F-69622, France
| | - Thibault Meyer
- Université Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Ecologie Microbienne, Villeurbanne F-69622, France
| | - Sabine Favre-Bonté
- Université Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Ecologie Microbienne, Villeurbanne F-69622, France
| | - Sylvie Nazaret
- Université Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Ecologie Microbienne, Villeurbanne F-69622, France
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77
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Goff JL, Lui LM, Nielsen TN, Poole FL, Smith HJ, Walker KF, Hazen TC, Fields MW, Arkin AP, Adams MWW. Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes. ISME COMMUNICATIONS 2024; 4:ycae064. [PMID: 38800128 PMCID: PMC11128244 DOI: 10.1093/ismeco/ycae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/11/2024] [Indexed: 05/29/2024]
Abstract
Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.
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Affiliation(s)
- Jennifer L Goff
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
| | - Heidi J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
| | - Kathleen F Walker
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37916, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37916, United States
- Genome Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Bioengineering, University of California, Berkeley, CA 94720, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
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78
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Song J, Chen Y, Mi H, Xu R, Zhang W, Wang C, Rensing C, Wang Y. Prevalence of antibiotic and metal resistance genes in phytoremediated cadmium and zinc contaminated soil assisted by chitosan and Trichoderma harzianum. ENVIRONMENT INTERNATIONAL 2024; 183:108394. [PMID: 38128385 DOI: 10.1016/j.envint.2023.108394] [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: 09/18/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Heavy metal in soil have been shown to be toxic with high concentrations and acts as selective pressure on both bacterial metal and antibiotic resistance determinants, posing a serious risk to public health. In cadmium (Cd) and zinc (Zn) contaminated soil, chitosan (Chi) and Trichoderma harzianum (Tri) were applied alone and in combination to assist phytoremediation by Amaranthus hypochondriacus L. Prevalence of antibiotic and metal resistance genes (ARGs and MRGs) in the soil was also evaluated using metagenomic approach. Results indicated that the phytoremediation of Cd and Zn contaminated soil was promoted by Chi, and Tri further reinforced this effect, along with the increased availability of Cd and Zn in soil. Meanwhile, combination of Chi and Tri enhanced the prevalence of ARGs (e.g., multidrug and β-lactam resistance genes) and maintained a high level of MRGs (e.g., chromium, copper) in soil. Soil available Zn and Cd fractions were the main factors contributing to ARGs profile by co-selection, while boosted bacterial hosts (e.g., Mitsuaria, Solirubrobacter, Ramlibacter) contributed to prevalence of most MRGs (e.g., Cd). These findings indicate the potential risk of ARGs and MRGs propagation in phytoremediation of metal contaminated soils assisted by organic and biological agents.
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Affiliation(s)
- Jianxiao Song
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China; Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, Xi'an 710000, Shaanxi, PR China
| | - Yanlong Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China; Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, Xi'an 710000, Shaanxi, PR China.
| | - Huizi Mi
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China
| | - Risheng Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China; Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, Xi'an 710000, Shaanxi, PR China
| | - Wenshuang Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China
| | - Chao Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China; Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, Xi'an 710000, Shaanxi, PR China
| | - Christopher Rensing
- Institute of Environmental Microbiology, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Yuheng Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China; Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, Xi'an 710000, Shaanxi, PR China
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79
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Bodus B, O'Malley K, Dieter G, Gunawardana C, McDonald W. Review of emerging contaminants in green stormwater infrastructure: Antibiotic resistance genes, microplastics, tire wear particles, PFAS, and temperature. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167195. [PMID: 37777137 DOI: 10.1016/j.scitotenv.2023.167195] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/08/2023] [Accepted: 09/16/2023] [Indexed: 10/02/2023]
Abstract
Green stormwater infrastructure is a growing management approach to capturing, infiltrating, and treating runoff at the source. However, there are several emerging contaminants for which green stormwater infrastructure has not been explicitly designed to mitigate and for which removal mechanisms are not yet well defined. This is an issue, as there is a growing understanding of the impact of emerging contaminants on human and environmental health. This paper presents a review of five emerging contaminants - antibiotic resistance genes, microplastics, tire wear particles, PFAS, and temperature - and seeks to improve our understanding of how green stormwater infrastructure is impacted by and can be designed to mitigate these emerging contaminants. To do so, we present a review of the source and transport of these contaminants to green stormwater infrastructure, specific treatment mechanisms within green infrastructure, and design considerations of green stormwater infrastructure that could lead to their removal. In addition, common removal mechanisms across these contaminants and limitations of green infrastructure for contaminant mitigation are discussed. Finally, we present future research directions that can help to advance the use of green infrastructure as a first line of defense for downstream water bodies against emerging contaminants of concern.
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Affiliation(s)
- Benjamin Bodus
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
| | - Kassidy O'Malley
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
| | - Greg Dieter
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
| | - Charitha Gunawardana
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
| | - Walter McDonald
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
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80
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Wang M, Masoudi A, Wang C, Wu C, Zhang Z, Zhao X, Liu Y, Yu Z, Liu J. Impacts of net cages on pollutant accumulation and its consequence on antibiotic resistance genes (ARGs) dissemination in freshwater ecosystems: Insights for sustainable urban water management. ENVIRONMENT INTERNATIONAL 2024; 183:108357. [PMID: 38056093 DOI: 10.1016/j.envint.2023.108357] [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: 06/10/2023] [Revised: 11/08/2023] [Accepted: 11/26/2023] [Indexed: 12/08/2023]
Abstract
There has been increasing interest in the role of human activities in disseminating antibiotic-resistance genes (ARGs) in aquatic ecosystems. However, the influence of pollutant accumulation on anthropogenic pollutant-ARG synergistic actions is limited. This study explored the association of net cages with the propagation of anthropogenic pollutants and their consequences for influencing the enrichment of ARGs using high-throughput metagenomic sequencing. We showed that net cages could substantially impact the ecology of freshwater systems by enhancing i) ARG diversity and the tendency for ARG-horizontal gene transfer and ii) the overlap of mobile genetic elements (MGEs) with biocide-metal resistance genes (BMRGs) and ARGs. These findings suggested that the cotransfer of these three genetic determinants would be favored in net cage plots and that nonantibiotic factors such as metal(loid)s, particularly iron (Fe), displayed robust selective pressures on ARGs exerted by the net cage. The resistome risk scores of net cage sediments and biofilms were higher than those from off-net cage plots, indicating that the net cage-origin antibiotic resistome should be of great concern. The combination of deterministic and stochastic processes acting on bacterial communities could explain the higher ARG variations in cage plots (8.2%) than in off-cage plots (3.4%). Moreover, MGEs and pollutants together explained 43.3% of the total variation in ARG communities, which was higher than that of off-cage plots (8.8%), considering pollutants, environmental variables, MGEs, and assembly processes. These findings will inform the development of policies and guidelines to more effectively limit the spread of antimicrobial resistance and achieve the goal of sustainability in freshwater systems in urban areas.
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Affiliation(s)
- Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Abolfazl Masoudi
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China.
| | - Can Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Changhao Wu
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Ze Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Xin Zhao
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Yuanjie Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China.
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China.
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81
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Sajjad W, Ali B, Niu H, Ilahi N, Rafiq M, Bahadur A, Banerjee A, Kang S. High prevalence of antibiotic-resistant and metal-tolerant cultivable bacteria in remote glacier environment. ENVIRONMENTAL RESEARCH 2023; 239:117444. [PMID: 37858689 DOI: 10.1016/j.envres.2023.117444] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/04/2023] [Accepted: 10/17/2023] [Indexed: 10/21/2023]
Abstract
Studies of antibiotic-resistant bacteria (ARB) have mainly originated from anthropic-influenced environments, with limited information from pristine environments. Remote cold environments are major reservoirs of ARB and have been determined in polar regions; however, their abundance in non-polar cold habitats is underexplored. This study evaluated antibiotics and metals resistance profiles, prevalence of antibiotic resistance genes (ARGs) and metals tolerance genes (MTGs) in 38 ARB isolated from the glacier debris and meltwater from Baishui Glacier No 1, China. Molecular identification displayed Proteobacteria (39.3%) predominant in debris, while meltwater was dominated by Actinobacteria (30%) and Proteobacteria (30%). Bacterial isolates exhibited multiple antibiotic resistance index values > 0.2. Gram-negative bacteria displayed higher resistance to antibiotics and metals than Gram-positive. PCR amplification exhibited distinct ARGs in bacteria dominated by β-lactam genes blaCTX-M (21.1-71.1%), blaACC (21.1-60.5%), tetracycline-resistant gene tetA (21.1-60.5%), and sulfonamide-resistant gene sulI (18.4-52.6%). Moreover, different MTGs were reported in bacterial isolates, including mercury-resistant merA (21.1-63.2%), copper-resistant copB (18.4-57.9%), chromium-resistant chrA (15.8-44.7%) and arsenic-resistant arsB (10.5-44.7%). This highlights the co-selection and co-occurrence of MTGs and ARGs in remote glacier environments. Different bacteria shared same ARGs, signifying horizontal gene transfer between species. Strong positive correlation among ARGs and MTGs was reported. Metals tolerance range exhibited that Gram-negative and Gram-positive bacteria clustered distinctly. Gram-negative bacteria were significantly tolerant to metals. Amino acid sequences of blaACC,blaCTX-M,blaSHV,blaampC,qnrA, sulI, tetA and blaTEM revealed variations. This study presents promising ARB, harboring ARGs with variations in amino acid sequences, highlighting the need to assess the transcriptome study of glacier bacteria conferring ARGs and MTGs.
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Affiliation(s)
- Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Barkat Ali
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Hewen Niu
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China; National Field Science Observation and Research Station of Yulong Snow Mountain Cryosphere and Sustainable Development, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Nikhat Ilahi
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Engineering and Management Sciences, Balochistan University of Information Technology, Quetta, Pakistan
| | - Ali Bahadur
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Abhishek Banerjee
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
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82
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Balcha ES, Gómez F, Gemeda MT, Bekele FB, Abera S, Cavalazzi B, Woldesemayat AA. Shotgun Metagenomics-Guided Prediction Reveals the Metal Tolerance and Antibiotic Resistance of Microbes in Poly-Extreme Environments in the Danakil Depression, Afar Region. Antibiotics (Basel) 2023; 12:1697. [PMID: 38136731 PMCID: PMC10740858 DOI: 10.3390/antibiotics12121697] [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: 10/30/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
The occurrence and spread of antibiotic resistance genes (ARGs) in environmental microorganisms, particularly in poly-extremophilic bacteria, remain underexplored and have received limited attention. This study aims to investigate the prevalence of ARGs and metal resistance genes (MRGs) in shotgun metagenome sequences obtained from water and salt crust samples collected from Lake Afdera and the Assale salt plain in the Danakil Depression, northern Ethiopia. Potential ARGs were characterized by the comprehensive antibiotic research database (CARD), while MRGs were identified by using BacMetScan V.1.0. A total of 81 ARGs and 39 MRGs were identified at the sampling sites. We found a copA resistance gene for copper and the β-lactam encoding resistance genes were the most abundant the MRG and ARG in the study area. The abundance of MRGs is positively correlated with mercury (Hg) concentration, highlighting the importance of Hg in the selection of MRGs. Significant correlations also exist between heavy metals, Zn and Cd, and ARGs, which suggests that MRGs and ARGs can be co-selected in the environment contaminated by heavy metals. A network analysis revealed that MRGs formed a complex network with ARGs, primarily associated with β-lactams, aminoglycosides, and tetracyclines. This suggests potential co-selection mechanisms, posing concerns for both public health and ecological balance.
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Affiliation(s)
- Ermias Sissay Balcha
- School of Medical Laboratory Science, College of Medicine and Health Sciences, Hawassa University, Hawassa P.O. Box 1560, Ethiopia;
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa P.O. Box 16417, Ethiopia;
| | - Felipe Gómez
- Centro de Astrobiología (INTA-CSIC) Crtera, Ajalvir km 4 Torrejón de Ardoz, P.O. Box 28850 Madrid, Spain;
| | - Mesfin Tafesse Gemeda
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa P.O. Box 16417, Ethiopia;
| | - Fanuel Belayneh Bekele
- School of Public Health, College of Medicine and Health Sciences, Hawassa University, Hawassa P.O. Box 1560, Ethiopia;
| | - Sewunet Abera
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands;
- Institute of Biology, Leiden University, P.O. Box 9500, 2300 RA Leiden, The Netherlands
- Ethiopian Institute of Agricultural Research (EIAR), Addis Ababa P.O. Box 2003, Ethiopia
| | - Barbara Cavalazzi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, 40100 Bologna, Italy;
- Department of Geology, University of Johannesburg, Johannesburg P.O. Box 524, South Africa
| | - Adugna Abdi Woldesemayat
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa P.O. Box 16417, Ethiopia;
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83
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Islam TN, Meem FS, Yasmin R, Amin MB, Rahman T, Mohasin M. Co-exposure of chromium or cadmium and a low concentration of amoxicillin are responsible to emerge amoxicillin resistant Staphylococcus aureus. J Glob Antimicrob Resist 2023; 35:279-288. [PMID: 37879458 DOI: 10.1016/j.jgar.2023.10.011] [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: 02/28/2023] [Revised: 10/04/2023] [Accepted: 10/14/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Heavy metals and antimicrobials co-exist in many environmental settings. The co-exposure of heavy metals and antimicrobials can drive emergence of antimicrobial resistant (AMR) Enterobacteriaceae. We hypothesized that co-exposure to heavy metals and a low concentration of antibiotic might alter antimicrobial susceptibility patterns, which facilitate emergence of AMR Staphylococcus aureus. METHODS The growth kinetics of antimicrobial susceptible S. aureus was carried out in the presence of chromium or cadmium salt and a low concentration of antibiotics. Subsequently, the antimicrobial susceptibility pattern was determined by the Kirby-Bauer disc diffusion method. Moreover, the mRNA copy number was determined by reverse transcription polymerase chain reaction. RESULTS The antimicrobial susceptibility profile revealed that the zone of inhibition (ZOI) for ampicillin, amoxicillin, ciprofloxacin and doxycycline was significantly decreased in chromium pre-exposed S. aureus compared to unexposed bacteria, whereas cadmium pre-exposed bacteria only showed significant decreased in ZOI for amoxicillin. Moreover, the MIC of amoxicillin for S. aureus was increased by 8-fold in chromium and 32-fold in cadmium when bacteria were co-exposed with low concentrations of amoxicillin. The mRNA expression of femX, mepA and norA also significantly increased in S. aureus after exposure to chromium and a low concentration of amoxicillin. CONCLUSION Cultivation of S. aureus at the minimum levels of chromium or cadmium and a low concentration of amoxicillin increased the inhibitory concentration of amoxicillin through inducing bacterial efflux pumps and antibiotic resistant genes. However, it is warranted to assess the whole transcriptome to find out all responsible factors behind this de novo amoxicillin resistant S. aureus.
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Affiliation(s)
- Tajreen Naziba Islam
- Infection and Immunity Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Foujia Samsad Meem
- Infection and Immunity Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Rahena Yasmin
- Infection and Immunity Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh; Department of Microbiology, University of Alabama at Birmingham, Alabama
| | - Mohammed Badrul Amin
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Tania Rahman
- Infection and Immunity Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md Mohasin
- Infection and Immunity Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh.
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84
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Joseph OJ, Ogunleye GE, Oyinlola KA, Balogun AI, Olumeko DT. Co-occurrence of heavy metals and antibiotics resistance in bacteria isolated from metal-polluted soil. Environ Anal Health Toxicol 2023; 38:e2023024-0. [PMID: 38298043 PMCID: PMC10834071 DOI: 10.5620/eaht.2023024] [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: 08/01/2023] [Accepted: 10/20/2023] [Indexed: 02/02/2024] Open
Abstract
The indiscriminate deposition of metal-containing substances into the environment contributes significantly to high concentrations of metals in the soil resulting in resistance to metals and consequentially to antibiotics by inherent microbes which may eventually spread to other pathogenic microbes thereby elevating disease burden due to antibiotic resistance. The study aimed at determining the co-occurrence of resistance of bacteria isolated from metal-contaminated soil to heavy metals and subsequently, antibiotics. Metal-tolerant bacteria were randomly isolated from top soils from a battery waste site using the pour plate method. Selected isolates were identified using biochemical tests, then, subjected to elevating supplemented concentrations of different metal salts at 100-500 μg/mL to determine the minimum inhibitory concentration. Isolates tolerant to minimum three metals up to 400 μg/mL were subjected to Sulfamethoxazole-trimethoprim (25 μg), Imipenem (10 μg), Amoxicillin (30 μg), Ciprofloxacin (10 μg) and Tigecycline (15 μg) and observations interpreted using the guiding principle of the Clinical and Laboratory Standards Institute. Metal concentrations in the soils exceeded permissible limits. In total, 16 isolates were selected and identified as Proteus sp. (1), Pseudomonas spp. (5), Enterobacter spp. (2), Klebsiella spp. (2), Escherichia spp. (3), Raoultella spp. (2) and Rahnella sp. (1). Thirteen (81.25 %) of all isolates showed multi-resistance to the metals and seven exhibited multidrug-resistance, with 4 (57.1 %) showing resistance to three different classes of antibiotics and 3 (42.9 %) showed resistance to four antibiotic classes. Heavy metal-tolerant bacteria isolated from this study possess co-selection potentials as they showed resistance to different metals and antibiotics classes which is a concern to public health.
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Affiliation(s)
- Oluwarotimi John Joseph
- Department of Biological Sciences, Faculty of Applied Sciences, KolaDaisi University, Ibadan, Nigeria
| | | | | | - Augustina I. Balogun
- Department of Biological Sciences, Faculty of Applied Sciences, KolaDaisi University, Ibadan, Nigeria
| | - Damilola Tolulope Olumeko
- Department of Biological Sciences, Faculty of Applied Sciences, KolaDaisi University, Ibadan, Nigeria
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85
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Lear L, Padfield D, Hesse E, Kay S, Buckling A, Vos M. Copper reduces the virulence of bacterial communities at environmentally relevant concentrations. ENVIRONMENT INTERNATIONAL 2023; 182:108295. [PMID: 37980880 DOI: 10.1016/j.envint.2023.108295] [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: 07/05/2023] [Revised: 09/13/2023] [Accepted: 10/27/2023] [Indexed: 11/21/2023]
Abstract
Increasing environmental concentrations of metals as a result of anthropogenic pollution are significantly changing many microbial communities. While there is evidence metal pollution can result in increased antibiotic resistance, the effects of metal pollution on the virulence of bacterial communities remains largely undetermined. Here, we experimentally test whether metal stress alters the virulence of bacterial communities. We do this by incubating three wastewater influent communities under different environmentally relevant copper concentrations for three days. We then quantify the virulence of the community phenotypically using the Galleria mellonella infection model, and test if differences are due to changes in the rate of biomass accumulation (productivity), copper resistance, or community composition (quantified using 16S amplicon sequencing). The virulence of the communities was found to be reduced by the highest copper concentration, but not to be affected by the lower concentration. As well as reduced virulence, communities exposed to the highest copper concentration were less diverse and had lower productivity. This work highlights that metal pollution may decrease virulence in bacterial communities, but at a cost to diversity and productivity.
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Affiliation(s)
- Luke Lear
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, United Kingdom.
| | - Dan Padfield
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, United Kingdom
| | - Elze Hesse
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, United Kingdom
| | - Suzanne Kay
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, United Kingdom
| | - Angus Buckling
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, United Kingdom
| | - Michiel Vos
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, United Kingdom
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86
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Silva-Holguín P, Medellín-Castillo NA, Zaragoza-Contreras EA, Reyes-López SY. Alumina-Hydroxyapatite Millimetric Spheres for Cadmium(II) Removal in Aqueous Medium. ACS OMEGA 2023; 8:44675-44688. [PMID: 38046353 PMCID: PMC10688153 DOI: 10.1021/acsomega.3c05418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/16/2023] [Accepted: 10/24/2023] [Indexed: 12/05/2023]
Abstract
Heavy metals can act as selective agents in the development and proliferation of antibiotic-resistant bacteria through a process called coselection. In the year 2050, an estimated 10 million deaths will be caused by antibiotic-resistant bacteria; therefore, the presence of heavy metals in bodies of water represents an environmental and sanitary threat that requires efficient treatment processes and/or materials for their removal. In the present study, the effect of the hydroxyapatite coating on the adsorbent capacity of cadmium in alumina spheres was evaluated. The hydroxyapatite coating on the alumina sphere increased the surface area from 0.66 to 0.96 m2/g and the number of acid sites from 0.064 to 0.306 meq/g and displaced the IEP of hydroxyapatite from 5.37 to 4.2, increasing the Cd2+ adsorbing capacity from 59.87 mg/g to 89.37 mg/g and promoting adsorption by surface complexation. Alumina-hydroxyapatite spheres stand out for their improved adsorbent properties and easy handling, which positioned this material as a potential alternative in adsorption processes.
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Affiliation(s)
- Pamela
Nair Silva-Holguín
- Laboratorio
de Materiales Híbridos Nanoestructurados, Departamento de Ciencias
Químico-Biológicas, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Envolvente del PRONAF y Estocolmo
s/n, Ciudad Juárez 32300, Mexico
| | - Nahum A. Medellín-Castillo
- Multidisciplinary
Graduate Program in Environmental Sciences, Autonomous University of San Luis Potosi, 78210 San Luis Potosi, Mexico
- Faculty
of Engineering, Graduate Studies and Research Center, Autonomous University of San Luis Potosi, 78290 San Luis Potosi, Mexico
| | - E. Armando Zaragoza-Contreras
- Centro
de Investigación en Materiales Avanzados SC, Miguel de Cervantes No. 120, Complejo
Industrial Chihuahua, Chihuahua 31136, Mexico
| | - Simón Yobanny Reyes-López
- Laboratorio
de Materiales Híbridos Nanoestructurados, Departamento de Ciencias
Químico-Biológicas, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Envolvente del PRONAF y Estocolmo
s/n, Ciudad Juárez 32300, Mexico
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87
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Abstract
Antibiotic resistance genes predate the therapeutic uses of antibiotics. However, the current antimicrobial resistance crisis stems from our extensive use of antibiotics and the generation of environmental stressors that impose new selective pressure on microbes and drive the evolution of resistant pathogens that now threaten human health. Similar to climate change, this global threat results from human activities that change habitats and natural microbiomes, which in turn interact with human-associated ecosystems and lead to adverse impacts on human health. Human activities that alter our planet at global scales exacerbate the current resistance crisis and exemplify our central role in large-scale changes in which we are both protagonists and architects of our success but also casualties of unanticipated collateral outcomes. As cognizant participants in this ongoing planetary experiment, we are driven to understand and find strategies to curb the ongoing crises of resistance and climate change.
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Affiliation(s)
- María Mercedes Zambrano
- Corpogen Research Center, Bogotá, Colombia;
- Dirección de Investigaciones y Transferencia de Conocimiento, Universidad Central, Bogotá, Colombia
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88
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Miao J, Ling Y, Chen X, Wu S, Liu X, Xu S, Umar S, Anderson BD. Assessing the nonlinear association of environmental factors with antibiotic resistance genes (ARGs) in the Yangtze River Mouth, China. Sci Rep 2023; 13:20367. [PMID: 37989759 PMCID: PMC10663556 DOI: 10.1038/s41598-023-45973-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
The emergence of antibacterial resistance (ABR) is an urgent and complex public health challenge worldwide. Antibiotic resistant genes (ARGs) are considered as a new pollutant by the WHO because of their wide distribution and emerging prevalence. The role of environmental factors in developing ARGs in bacterial populations is still poorly understood. Therefore, the relationship between environmental factors and bacteria should be explored to combat ABR and propose more tailored solutions in a specific region. Here, we collected and analyzed surface water samples from Yangtze Delta, China during 2021, and assessed the nonlinear association of environmental factors with ARGs through a sigmoid model. A high abundance of ARGs was detected. Amoxicillin, phosphorus (P), chromium (Cr), manganese (Mn), calcium (Ca), and strontium (Sr) were found to be strongly associated with ARGs and identified as potential key contributors to ARG detection. Our findings suggest that the suppression of ARGs may be achieved by decreasing the concentration of phosphorus in surface water. Additionally, Group 2A light metals (e.g., magnesium and calcium) may be candidates for the development of eco-friendly reagents for controlling antibiotic resistance in the future.
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Affiliation(s)
- Jiazheng Miao
- Division of Natural and Applied Science, Duke Kunshan University, Kunshan, Jiangsu, China
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yikai Ling
- Division of Natural and Applied Science, Duke Kunshan University, Kunshan, Jiangsu, China
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Xiaoyuan Chen
- Division of Natural and Applied Science, Duke Kunshan University, Kunshan, Jiangsu, China
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Siyuan Wu
- Division of Natural and Applied Science, Duke Kunshan University, Kunshan, Jiangsu, China
- Department of Statistics, University of Michigan, Ann Arbor, MI, USA
| | - Xinyue Liu
- Division of Natural and Applied Science, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Shixin Xu
- Division of Natural and Applied Science, Duke Kunshan University, Kunshan, Jiangsu, China
- Global Health Research Center, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Sajid Umar
- Division of Natural and Applied Science, Duke Kunshan University, Kunshan, Jiangsu, China
- Global Health Research Center, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Benjamin D Anderson
- Division of Natural and Applied Science, Duke Kunshan University, Kunshan, Jiangsu, China.
- Global Health Research Center, Duke Kunshan University, Kunshan, Jiangsu, China.
- Department of Environmental and Global Health, College of Public Health and Health Professions, and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32610, USA.
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Tseng AS, Roberts MC, Weissman SJ, Rabinowitz PM. Study of heavy metal resistance genes in Escherichia coli isolates from a marine ecosystem with a history of environmental pollution (arsenic, cadmium, copper, and mercury). PLoS One 2023; 18:e0294565. [PMID: 37972039 PMCID: PMC10653420 DOI: 10.1371/journal.pone.0294565] [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: 06/06/2023] [Accepted: 11/04/2023] [Indexed: 11/19/2023] Open
Abstract
We analyzed whole genome sequences of 308 Escherichia coli isolates from a marine ecosystem to determine the prevalence and relationships of heavy metal resistance genes (HMRGs) and antibiotic resistance genes (ARGs), as well as the presence of plasmid sequences. We screened all genomes for presence of 18 functional HMRGs conferring resistance to arsenic, cadmium, copper, or cadmium/mercury. In subset analyses, we examined geographic variations of HMRG carriage patterns in 224 isolates from water sources, and sought genetic linkages between HMRGs and ARGs in 25 genomes of isolates resistant to antibiotics. We found high carriage rates of HMRGs in all genomes, with 100% carrying at least one copy of 11 out of 18 HMRGs. A total of 173 (56%) of the isolates carried both HMRGs and plasmid sequences. In the 25 genomes of antibiotic-resistant isolates, 80% (n = 20) carried HMRGs, ARGs, and plasmid sequences, while 40% (n = 10) had linked HMRGs and ARGs on their assembled genomes. We found no evidence of geographic variation in HMRG frequency, nor any association between locational proximity to Superfund sites and co-carriage of HMRGs and ARGs. Our study findings indicate that HMRGs are common among E. coli in marine ecosystems, suggesting widespread heavy metal presence in water sources of a region with history of environmental pollution. Further research is needed to determine the role HMRGs play in driving antimicrobial resistance in human pathogens through genetic linkage and the value their detection in environmental bacterial genomes may offer as an indicator of environmental heavy metal pollution.
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Affiliation(s)
- Ashley S. Tseng
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Marilyn C. Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Scott J. Weissman
- Division of Infectious Diseases, Seattle Children’s Hospital, Seattle, Washington, United States of America
| | - Peter M. Rabinowitz
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
- Center for One Health Research, Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
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90
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Fu S, Zhang Y, Wang R, Qiu Z, Song W, Yang Q, Shen L. A novel culture-enriched metagenomic sequencing strategy effectively guarantee the microbial safety of drinking water by uncovering the low abundance pathogens. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118737. [PMID: 37657296 DOI: 10.1016/j.jenvman.2023.118737] [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: 04/02/2023] [Revised: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 09/03/2023]
Abstract
Assessing the presence of waterborne pathogens and antibiotic resistance genes (ARGs) is crucial for managing the environmental quality of drinking water sources. However, detecting low abundance pathogens in such settings is challenging. In this study, a workflow was developed to enrich for broad spectrum pathogens from drinking water samples. A mock community was used to evaluate the effectiveness of various enrichment broths in detecting low-abundance pathogens. Monthly metagenomic surveillance was conducted in a drinking water source from May to September 2021, and water samples were subjected to five enrichment procedures for 6 h to recover the majority of waterborne bacterial pathogens. Oxford Nanopore Technology (ONT) was used for metagenomic sequencing of enriched samples to obtain high-quality pathogen genomes. The results showed that selective enrichment significantly increased the proportions of targeted bacterial pathogens. Compared to direct metagenomic sequencing of untreated water samples, targeted enrichment followed by ONT sequencing significantly improved the detection of waterborne pathogens and the quality of metagenome-assembled genomes (MAGs). Eighty-six high-quality MAGs, including 70 pathogen MAGs, were obtained from ONT sequencing, while only 12 MAGs representing 10 species were obtained from direct metagenomic sequencing of untreated water samples. In addition, ONT sequencing improved the recovery of mobile genetic elements and the accuracy of phylogenetic analysis. This study highlights the urgent need for efficient methodologies to detect and manage microbial risks in drinking water sources. The developed workflow provides a cost-effective approach for environmental management of drinking water sources with microbial risks. The study also uncovered pathogens that were not detected by traditional methods, thereby advancing microbial risk management of drinking water sources.
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Affiliation(s)
- Songzhe Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, 710069, China; Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 116023, China.
| | - Yixiang Zhang
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences. Shanghai, China; University of Chinese Academy of Sciences, Shanghai, China
| | - Rui Wang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 116023, China
| | - Zhiguang Qiu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Weizhi Song
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, SAR, Hong Kong, China
| | - Qian Yang
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Lixin Shen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, 710069, China.
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91
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Li L, Guan W, Fan Y, He Q, Guo D, Yuan A, Xing Q, Wang Y, Ma Z, Ni J, Chen J, Zhou Q, Zhong Y, Li J, Zhang H. Zinc/carbon nanomaterials inhibit antibiotic resistance genes by affecting quorum sensing and microbial community in cattle manure production. BIORESOURCE TECHNOLOGY 2023; 387:129648. [PMID: 37572887 DOI: 10.1016/j.biortech.2023.129648] [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: 04/18/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 08/14/2023]
Abstract
This study used metagenomic sequencing to examine the effects of carbon-based zinc oxide nanoparticles (CZnONPs) and graphene-based zinc oxide nanoparticles (GZnONPs) on quorum sensing (QS), antibiotic resistance genes (ARGs) and microbial community changes during cattle manure production. The manure zinc content was significantly reduced in GZnONPs group. In the QS pathway, the autoinducer gene increases significantly in Control group, while the transporter and repressor genes experience a substantial increase in CZnONPs group. These results contributed to the significantly decreased the abundance of ARGs in GZnONPs group. The co-occurrence network analysis revealed a correlation between core ARGs and QS-related KEGG Orthology or ARGs' hosts, indicating that the selective pressure of zinc influences microbial QS, forming a unique ARG pattern in in vivo anaerobic fermentation. These findings suggest that implementing nutritional regulation in farming practices can serve as a preventive measure to mitigate the potential transmission of ARGs resulting from livestock waste.
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Affiliation(s)
- Lizhi Li
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Weikun Guan
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Yihao Fan
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Qin He
- College of Life Sciences, Nanchang Normal University, Nanchang 330032, China
| | - Dongsheng Guo
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - An Yuan
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Qingfeng Xing
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Yang Wang
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Ziqin Ma
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Jian Ni
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Jia Chen
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Qilong Zhou
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Yuhong Zhong
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Jiating Li
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Haibo Zhang
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China.
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92
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Sun H, Li H, Zhang X, Liu Y, Chen H, Zheng L, Zhai Y, Zheng H. The honeybee gut resistome and its role in antibiotic resistance dissemination. Integr Zool 2023; 18:1014-1026. [PMID: 36892101 DOI: 10.1111/1749-4877.12714] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
There is now general concern about widespread antibiotic resistance, and growing evidence indicates that gut microbiota is critical in providing antibiotic resistance. Honeybee is an important pollinator; the incidence of antibiotic resistance genes in honeybee gut causes potential risks to not only its own health but also to public and animal health, for its potential disseminator role, thus receiving more attention from the public. Recent analysis results reveal that the gut of honeybee serves as a reservoir of antibiotic resistance genes, probably due to antibiotics application history in beekeeping and horizontal gene transfer from the highly polluted environment. These antibiotic resistance genes accumulate in the honeybee gut and could be transferred to the pathogen, even having the potential to spread during pollination, tending, social interactions, etc. Newly acquired resistance traits may cause fitness reduction in bacteria whereas facilitating adaptive evolution as well. This review outlines the current knowledge about the resistome in honeybee gut and emphasizes its role in antibiotic resistance dissemination.
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Affiliation(s)
- Huihui Sun
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Hu Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yan Liu
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Hao Chen
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Li Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Yifan Zhai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Hao Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
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93
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Kimbell LK, LaMartina EL, Kohls S, Wang Y, Newton RJ, McNamara PJ. Impact of corrosion inhibitors on antibiotic resistance, metal resistance, and microbial communities in drinking water. mSphere 2023; 8:e0030723. [PMID: 37681947 PMCID: PMC10597465 DOI: 10.1128/msphere.00307-23] [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: 06/20/2023] [Accepted: 07/17/2023] [Indexed: 09/09/2023] Open
Abstract
Corrosion inhibitors, including zinc orthophosphate, sodium orthophosphate, and sodium silicate, are commonly used to prevent the corrosion of drinking water infrastructure. Metals such as zinc are known stressors for antibiotic resistance selection, and phosphates can increase microbial growth in drinking water distribution systems (DWDS). Yet, the influence of corrosion inhibitor type on antimicrobial resistance in DWDS is unknown. Here, we show that sodium silicates can decrease antibiotic resistant bacteria (ARB) and antibiotic-resistance genes (ARGs), while zinc orthophosphate increases ARB and ARGs in source water microbial communities. Based on controlled bench-scale studies, zinc orthophosphate addition significantly increased the abundance of ARB resistant to ciprofloxacin, sulfonamides, trimethoprim, and vancomycin, as well as the genes sul1, qacEΔ1, an indication of resistance to quaternary ammonium compounds, and the integron-integrase gene intI1. In contrast, sodium silicate dosage at 10 mg/L resulted in decreased bacterial growth and antibiotic resistance selection compared to the other corrosion inhibitor additions. Source water collected from the drinking water treatment plant intake pipe resulted in less significant changes in ARB and ARG abundance due to corrosion inhibitor addition compared to source water collected from the pier at the recreational beach. In tandem with the antibiotic resistance shifts, significant microbial community composition changes also occurred. Overall, the corrosion inhibitor sodium silicate resulted in the least selection for antibiotic resistance, which suggests it is the preferred corrosion inhibitor option for minimizing antibiotic resistance proliferation in DWDS. However, the selection of an appropriate corrosion inhibitor must also be appropriate for the water chemistry of the system (e.g., pH, alkalinity) to minimize metal leaching first and foremost and to adhere to the lead and copper rule. IMPORTANCE Antibiotic resistance is a growing public health concern across the globe and was recently labeled the silent pandemic. Scientists aim to identify the source of antibiotic resistance and control points to mitigate the spread of antibiotic resistance. Drinking water is a direct exposure route to humans and contains antibiotic-resistant bacteria and associated resistance genes. Corrosion inhibitors are added to prevent metallic pipes in distribution systems from corroding, and the type of corrosion inhibitor selected could also have implications on antibiotic resistance. Indeed, we found that sodium silicate can minimize selection of antibiotic resistance while phosphate-based corrosion inhibitors can promote antibiotic resistance. These findings indicate that sodium silicate is a preferred corrosion inhibitor choice for mitigation of antibiotic resistance.
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Affiliation(s)
- Lee K. Kimbell
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
| | - Emily Lou LaMartina
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Stan Kohls
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
| | - Yin Wang
- Department of Civil and Environmental Engineering, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Ryan J. Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Patrick J. McNamara
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
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94
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Wu J, Guo S, Lin H, Li K, Li Z, Wang J, Gaze WH, Zou J. Uncovering the prevalence and drivers of antibiotic resistance genes in soils across different land-use types. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118920. [PMID: 37660639 DOI: 10.1016/j.jenvman.2023.118920] [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: 06/05/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
The emergence and spread of antibiotic resistance genes (ARGs) in soil due to animal excreta and organic waste is a major threat to human health and ecosystems, and global efforts are required to tackle the issue. However, there is limited knowledge of the variation in ARG prevalence and diversity resulting from different land-use patterns and underlying driving factors in soils. This study aimed to comprehensively characterize the profile of ARGs and mobile genetic elements and their drivers in soil samples collected from 11 provinces across China, representing three different land-use types, using high-throughput quantitative polymerase chain reaction and 16S rRNA amplicon sequencing. Our results showed that agricultural soil had the highest abundance and diversity of ARGs, followed by tea plantation and forest land. A total of 124 unique ARGs were detected in all samples, with shared subtypes among different land-use patterns indicating a common origin or high transmission frequency. Moreover, significant differences in ARG distribution were observed among different geographical regions, with the greatest enrichment of ARGs found in southern China. Biotic and abiotic factors, including soil properties, climatic factors, and bacterial diversity, were identified as the primary drivers associated with ARG abundance, explaining 71.8% of total ARG variation. The findings of our study demonstrate that different land-use patterns are associated with variations in ARG abundance in soil, with agricultural practices posing the greatest risk to human health and ecosystems regarding ARGs. Our identification of biotic and abiotic drivers of ARG abundance provides valuable insights into strategies for mitigating the spread of these genes. This study emphasizes the need for coordinated and integrated approaches to address the global antimicrobial resistance crisis.
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Affiliation(s)
- Jie Wu
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shumin Guo
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haiyan Lin
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kejie Li
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhutao Li
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinyang Wang
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China.
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment & Sustainability Institute, Penryn Campus, TR10 9FE, United Kingdom
| | - Jianwen Zou
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
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95
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Wu L, Shen Z, Zhou Y, Zuo J. Stimulating anaerobic digestion to degrade recalcitrant organic pollutants: Potential role of conductive materials-led direct interspecies electron transfer. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118337. [PMID: 37343473 DOI: 10.1016/j.jenvman.2023.118337] [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: 03/28/2023] [Revised: 05/26/2023] [Accepted: 06/04/2023] [Indexed: 06/23/2023]
Abstract
This review aims to provide a comprehensive understanding of the potential of CMs-dominated DIET in the degradation of recalcitrant organic pollutants in AD. The review covers the mechanisms and efficiencies of recalcitrant organic pollutant degradation by CMs-dominated DIET, the comparison of degradation pathways between DIET and chemical treatment, recent insights on DIET-enhanced degradation, and the evaluation of the potential and future development of CMs-dominated DIET. The review emphasizes the importance of coupled syntrophic microorganisms, electron flux, and physicochemical properties of CMs in enhancing the degradation performance of AD. Additionally, it highlights the advantages of DIET-led syntrophic metabolism over traditional oxidation technologies in terms of environmental friendliness and efficiency. Finally, the review acknowledges the potential risks associated with introducing CMs into AD systems and provides guidance for waste treatment and energy recovery.
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Affiliation(s)
- Linjun Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environment Sciences, Beijing, 100012, China; Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Zhiqiang Shen
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environment Sciences, Beijing, 100012, China; Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Yuexi Zhou
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environment Sciences, Beijing, 100012, China; Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Jiane Zuo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China; Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, China.
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96
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Wu Z, Cai P, Liang E, Chen Q, Sun W, Wang J. Distinct adaptive strategies and microbial interactions of soil viruses under different metal(loid) contaminations. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132347. [PMID: 37619274 DOI: 10.1016/j.jhazmat.2023.132347] [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: 06/07/2023] [Revised: 08/05/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Viruses, as the most abundant organisms, significantly influence ecological function and microbial survival in soils, yet little was known about how viruses and virus-microbe interactions respond to environmental stresses induced by metal(loid) contaminations. Here, we conducted the metagenomic analysis to investigate the adaptative mechanisms of soil viruses under different metal(loid) contamination levels. By capturing a catalogue of 23,066 viruses, we found that viral communities exhibited the increased richness, diversity, and the temperate to lytic ratio in facing the highest metal(loid) contaminations. Meanwhile, viruses displayed obvious lineage-specific infection modes to distinct dominant hosts under different pollution levels. Viral functions linking to the inhibition of transcription and the enhancement of DNA repairment as well as multiple resistance not only contributed to coping with elevated multiple metal(loid) stresses, but also facilitated the adaptation and functioning of viral hosts. Moreover, the harmonious coexistence of viruses and resistant/pathogenic bacteria under the heaviest contaminations potentially exacerbated disseminating resistance and pathogenicity, while viruses under the lightest contaminations might be natural predators of resistant/pathogenic bacteria through lysing host cells. Overall, this study highlights the ecological importance of viral adaptation and the interactions between viruses and resistant/pathogenic bacteria in contaminated environments, contributing to developing virus-based approaches to soil restoration.
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Affiliation(s)
- Zongzhi Wu
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, China; School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Pinggui Cai
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Enhang Liang
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, China
| | - Weiling Sun
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, China
| | - Jiawen Wang
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, China; School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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97
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Zhang J, Xu Z, Chu W, Ju F, Jin W, Li P, Xiao R. Residual chlorine persistently changes antibiotic resistance gene composition and increases the risk of antibiotic resistance in sewer systems. WATER RESEARCH 2023; 245:120635. [PMID: 37738943 DOI: 10.1016/j.watres.2023.120635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 09/24/2023]
Abstract
During the COVID-19 pandemic, excessive amounts of disinfectants and their transformation products entered sewer systems worldwide, which was an extremely rare occurrence before. The stress of residual chlorine and disinfection by-products is not only likely to promote the spread of antibiotic resistance genes (ARGs), but also leads to the enrichment of chlorine-resistant bacteria that may also be resistant to antibiotics. Therefore, the potential impact of such discharge on ARG composition should be studied and the health risks should be assessed. Thus, this study combined high-throughput 16S rRNA gene amplicon sequencing and metagenomic analysis with long-term batch tests that involved two stages of stress and recovery to comprehensively evaluate the impact of residual chlorine on the microbial community and ARG compositions in sewer systems. The tests demonstrated that the disturbance of the microbial community structure by residual chlorine was reversible, but the change in ARG composition was persistent. This study found that vertical propagation and horizontal gene transfer jointly drove ARG composition succession in the biofilm, while the driving force was mainly horizontal gene transfer in the sediment. In this process, the biocide resistance gene (BRG) subtype chtR played an important role in promoting co-selection with ARGs through plasmids and integrative and conjugative elements. Moreover, it was further shown that the addition of sodium hypochlorite increased the risk of ARGs to human health, even after discontinuation of dosing, signifying that the impact was persistent. In general, this study strengthens the co-selection theory of ARGs and BRGs, and calls for improved disinfection strategies and more environmentally friendly disinfectants.
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Affiliation(s)
- Jingyi Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Ministry of Education Key Laboratory of Yangtze River Water Environment, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Zuxin Xu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Ministry of Education Key Laboratory of Yangtze River Water Environment, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| | - Wenhai Chu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Ministry of Education Key Laboratory of Yangtze River Water Environment, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Wei Jin
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Ministry of Education Key Laboratory of Yangtze River Water Environment, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Peng Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Ministry of Education Key Laboratory of Yangtze River Water Environment, Tongji University, Shanghai 200092, China; College of Resources and Environmental Engineering, Shandong Agriculture and Engineering University, Jinan, Shandong 250100, China
| | - Rong Xiao
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Ministry of Education Key Laboratory of Yangtze River Water Environment, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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Yan M, Zhu C, Yang Z, Li H. Pig manure-derived fulvic acid more strongly drives the fate of arsenic and antibiotic resistance genes in paddy soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118683. [PMID: 37531670 DOI: 10.1016/j.jenvman.2023.118683] [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: 02/04/2023] [Revised: 06/26/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023]
Abstract
Antibiotic resistance genes (ARGs) can threaten the clean production of rice owing to continuous selective pressure in heavy metal-antibiotic co-contaminated paddy soils. As an important soil carbon reservoir, the role of humic substances from different types of manure in the regulation of soil ARGs remains unclear. In this study, fulvic acid (FA) and humic acid (HA) were extracted from pig manure (PM), cow dung (CD), and chicken manure (CM). The influence of their characteristics and doses on the fate of ARGs was investigated in arsenic (As)-antibiotic co-contaminated paddy soils. The release of As and degradation of antibiotics were promoted in 1% PM-FA treatment, with increases of 4.8%-5.6% and 8.3%-8.8% compared with CM-FA and CD-FA treatments, respectively. The coexistence of FA/HA, Fe, As, and antibiotics in soil pore water affected the environmental behavior of ARGs, with FA showing a more positive effect. Species including Bacillus, Geobacter, Desulfitobacterium, and Christensenellaceae_R-7_group were considered potential hosts of ARGs, and their resistance to co-contamination increased after the addition of FA. Membrane transport is a potential strategy for host bacteria of ARGs to cope with As-antibiotic complex pressure. These results demonstrate the coupling mechanisms of As, antibiotics, and ARGs regulated by different humic substances in co-contaminated paddy soils, which could support the clean production of rice in agricultural practice.
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Affiliation(s)
- Mengmeng Yan
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China; National Navel Orange Engineering Research Center/School of Life Sciences, Gannan Normal University, Ganzhou, 341000, PR China.
| | - Changxiong Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
| | - Zhonglan Yang
- National Navel Orange Engineering Research Center/School of Life Sciences, Gannan Normal University, Ganzhou, 341000, PR China.
| | - Hongna Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
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99
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Li J, Li L, Li Q, Fang W, Sun Y, Lu Y, Wang J, Zhu Y, Zhang Y. Distribution and relationship of antibiotics, heavy metals and resistance genes in the upstream of Hanjiang River Basin in Shiyan, China. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:7115-7130. [PMID: 37453967 DOI: 10.1007/s10653-023-01683-9] [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: 03/28/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
The upstream basin of Hanjiang River is an important water source for the middle route of China's South-to-North Water Diversion Project. The quality of water and soil in the Hanjiang River have enormous biological and environmental impacts, and resistant genetic contamination has emerged, but only few studies are concerned the correlation between heavy metals and metal resistance genes (MRGs). In this study, 8 antibiotics and 19 heavy metals were analyzed, the results showed that the highest antibiotic content was tetracycline, with mean concentrations of 43.201 µg/kg and 0.022 µg/L. Mn was the highest heavy metal in soil with a content of 1408.284 µg/kg, and in water was Zn with a content of 10.611 µg/L. We found that the most abundant antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in the study area were bacA and arsT genes, coding for resistance mechanisms to bacitracin and arsenic, respectively. The data showed that heavy metals had a greater impact on antibiotic resistance genes than antibiotics, and the correlation between resistance genes was significantly positive. This work expands our understanding of the correlations of antibiotics, heavy metals, and resistance genes in the Hanjiang River, indicating that more attention should be paid to the effects of resistance genes and the quality of water.
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Affiliation(s)
- Jing Li
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China
| | - Lijuan Li
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China
| | - Qin Li
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China
| | - Wen Fang
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China
| | - Yonghao Sun
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China
| | - Yu Lu
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China
| | - Jing Wang
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China
| | - Yanrong Zhu
- Hanjiang Bureau of Hydrology and Water Resources Survey, Bureau of Hydrology, Changjiang Water Resources Commission, Xiangyang, 441022, People's Republic of China
| | - Yao Zhang
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China.
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100
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K S, Vasanthrao R, Chattopadhyay I. Impact of environment on transmission of antibiotic-resistant superbugs in humans and strategies to lower dissemination of antibiotic resistance. Folia Microbiol (Praha) 2023; 68:657-675. [PMID: 37589876 DOI: 10.1007/s12223-023-01083-7] [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: 12/26/2022] [Accepted: 08/02/2023] [Indexed: 08/18/2023]
Abstract
Antibiotics are the most efficient type of therapy developed in the twentieth century. From the early 1960s to the present, the rate of discovery of new and therapeutically useful classes of antibiotics has significantly decreased. As a result of antibiotic use, novel strains emerge that limit the efficiency of therapies in patients, resulting in serious consequences such as morbidity or mortality, as well as clinical difficulties. Antibiotic resistance has created major concern and has a greater impact on global health. Horizontal and vertical gene transfers are two mechanisms involved in the spread of antibiotic resistance genes (ARGs) through environmental sources such as wastewater treatment plants, agriculture, soil, manure, and hospital-associated area discharges. Mobile genetic elements have an important part in microbe selection pressure and in spreading their genes into new microbial communities; additionally, it establishes a loop between the environment, animals, and humans. This review contains antibiotics and their resistance mechanisms, diffusion of ARGs, prevention of ARG transmission, tactics involved in microbiome identification, and therapies that aid to minimize infection, which are explored further below. The emergence of ARGs and antibiotic-resistant bacteria (ARB) is an unavoidable threat to global health. The discovery of novel antimicrobial agents derived from natural products shifts the focus from chemical modification of existing antibiotic chemical composition. In the future, metagenomic research could aid in the identification of antimicrobial resistance genes in the environment. Novel therapeutics may reduce infection and the transmission of ARGs.
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Affiliation(s)
- Suganya K
- Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India
| | - Ramavath Vasanthrao
- Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India
| | - Indranil Chattopadhyay
- Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India.
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