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Wang F, Huang W, Zhang M, Zhang Q, Luo Y, Chen J, Su Y, Huang H, Fang F, Luo J. Disinfectant polyhexamethylene guanidine triggered simultaneous efflux pump antibiotic- and metal-resistance genes propagation during sludge anaerobic digestion. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 357:124453. [PMID: 38936038 DOI: 10.1016/j.envpol.2024.124453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/25/2024] [Accepted: 06/25/2024] [Indexed: 06/29/2024]
Abstract
The environmental transmission of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) exerted devastating threats to global public health, and their interactions with other emerging contaminants (ECs) have raised increasing concern. This study investigated that the abundances of ARGs and MRGs with the predominant type of efflux pump were simultaneously increased (8.4-59.1%) by disinfectant polyhexamethylene guanidine (PHMG) during waste activated sludge (WAS) anaerobic digestion. The aggregation of the same microorganisms (i.e., Hymenobacter and Comamonas) and different host bacteria (i.e., Azoarcus and Thauera) were occurred upon exposure to PHMG, thereby increasing the co-selection and propagation of MRGs and ARGs by vertical gene transfer. Moreover, PHMG enhanced the process of horizontal gene transfer (HGT), facilitating their co-transmission by the same mobile genetic elements (20.2-223.7%). Additionally, PHMG up-regulated the expression of critical genes (i.e., glnB, trpG and gspM) associated with the HGT of ARGs and MRGs (i.e., two-component regulatory system and quorum sensing) and exocytosis system (i.e., bacterial secretion system). Structural equation model analysis further verified that the key driver for the simultaneous enrichment of ARGs and MRGs under PHMG stress was microbial community structure. The study gives new insights into the aggravated environmental risks and mechanisms of ECs in sludge digestion system, providing guidance for subsequent regulation and control of ECs.
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Affiliation(s)
- Feng Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Wenxuan Huang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Meili Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Qin Zhang
- School of Energy and Environment, Anhui University of Technology, Ma'anshan, 243000, China
| | - Yuting Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Jiale Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Yinglong Su
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, China
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Fang Fang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Jingyang Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, China.
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Sivalingam P, Sabatino R, Sbaffi T, Corno G, Fontaneto D, Borgomaneiro G, Rogora M, Crotti E, Mapelli F, Borin S, Pilar AL, Eckert EM, Di Cesare A. Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134885. [PMID: 38876022 DOI: 10.1016/j.jhazmat.2024.134885] [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: 02/05/2024] [Revised: 04/19/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024]
Abstract
Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.
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Affiliation(s)
- Periyasamy Sivalingam
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy
| | - Raffaella Sabatino
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy; National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
| | - Tomasa Sbaffi
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy; National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
| | - Gianluca Corno
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy; National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
| | - Diego Fontaneto
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy; National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
| | - Giulia Borgomaneiro
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy
| | - Michela Rogora
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy
| | - Elena Crotti
- Department of Food Environmental and Nutritional Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Francesca Mapelli
- Department of Food Environmental and Nutritional Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Sara Borin
- Department of Food Environmental and Nutritional Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Andrea Lopez Pilar
- Biological Science Faculty, Complutense University of Madrid, Jose Antonio Novais 12, 28040 Madrid, Spain
| | - Ester M Eckert
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy; National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
| | - Andrea Di Cesare
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy; National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy.
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3
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Cai Y, Chen C, Sun T, Li G, Wang W, Zhao H, An T. Mariculture waters as yet another hotbed for the creation and transfer of new antibiotic-resistant pathogenome. ENVIRONMENT INTERNATIONAL 2024; 187:108704. [PMID: 38692150 DOI: 10.1016/j.envint.2024.108704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/11/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
With the rapid growth of aquaculture globally, large amounts of antibiotics have been used to treat aquatic disease, which may accelerate induction and spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in aquaculture environments. Herein, metagenomic and 16S rRNA analyses were used to analyze the potentials and co-occurrence patterns of pathogenome (culturable and unculturable pathogens), antibiotic resistome (ARGs), and mobilome (mobile genetic elements (MGEs)) from mariculture waters near 5000 km coast of South China. Total 207 species of pathogens were identified, with only 10 culturable species. Furthermore, more pathogen species were detected in mariculture waters than those in coastal waters, and mariculture waters were prone to become reservoirs of unculturable pathogens. In addition, 913 subtypes of 21 ARG types were also identified, with multidrug resistance genes as the majority. MGEs including plasmids, integrons, transposons, and insertion sequences were abundantly present in mariculture waters. The co-occurrence network pattern between pathogenome, antibiotic resistome, and mobilome suggested that most of pathogens may be potential multidrug resistant hosts, possibly due to high frequency of horizontal gene transfer. These findings increase our understanding of mariculture waters as reservoirs of antibiotic resistome and mobilome, and as yet another hotbed for creation and transfer of new antibiotic-resistant pathogenome.
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Affiliation(s)
- Yiwei Cai
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development (Department of Education), School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Chunliang Chen
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development (Department of Education), School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Tong Sun
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development (Department of Education), School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Guiying Li
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development (Department of Education), School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Wanjun Wang
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development (Department of Education), School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Huijun Zhao
- Centre for Clean Environment and Energy, and Griffith School of Environment, Gold Coast Campus, Griffith University, Queensland 4222, Australia
| | - Taicheng An
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development (Department of Education), School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
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Di Cesare A, Sabatino R, Sbaffi T, Fontaneto D, Brambilla D, Beghi A, Pandolfi F, Borlandelli C, Fortino D, Biccai G, Genoni P, Corno G. Anthropogenic pollution drives the bacterial resistome in a complex freshwater ecosystem. CHEMOSPHERE 2023; 331:138800. [PMID: 37121282 DOI: 10.1016/j.chemosphere.2023.138800] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/06/2023] [Accepted: 04/27/2023] [Indexed: 05/03/2023]
Abstract
Aquatic ecosystems in anthropogenically impacted areas are important reservoirs of antibiotic resistance genes (ARGs) of allochthonous origin. However, the dynamics of the different ARGs within the bacterial communities of lakes and rivers, as well as the factors that drive their selection, are not completely understood. In this study, we analysed the fate of the bacterial resistome (total content of ARGs and of metal resistance genes, MRGs) for a period of six months (summer-winter) in a continuum lake-river-lake system (Lake Varese, River Bardello, Lake Maggiore) in Northern Italy, by shotgun metagenomics. The metagenomic data were then compared with chemical, physical and microbiological data, to infer the role of anthropogenic pressure in the different sampling stations. ARGs and MRGs were more abundant and diverse in the River Bardello, characterised by the highest anthropogenic pollution. The date of sampling influenced ARGs and MRGs, with higher abundances in summer (August) than in fall or in winter, when the impact of the treated wastewater discharge in the river was limited by a higher water flow from Lake Varese. ARG and MRG abundances were significantly correlated and they co-occurred in the main network analysis modules with potential pathogenic bacteria. Different levels of anthropogenic impact selectively promoted specific ARGs while others, generally abundant in waters, were not affected by anthropogenic pressure. Reducing the level of anthropogenic pressure resulted in a rapid decrease of most ARGs. From our results, the role of anthropogenic pressure in promoting the spread of specific antibiotic resistances and of potential pathogens in aquatic ecosystem becomes clear. Finally we highlight the strict correlation between ARGs and MRGs suggesting their potential co-selection in stressed aquatic bacterial communities.
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Affiliation(s)
- Andrea Di Cesare
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Raffaella Sabatino
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Tomasa Sbaffi
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Diego Fontaneto
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Diego Brambilla
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Andrea Beghi
- Regional Environmental Protection Agency of Lombardia, Italy
| | - Franca Pandolfi
- Regional Environmental Protection Agency of Lombardia, Italy
| | | | - Davide Fortino
- Regional Environmental Protection Agency of Lombardia, Italy
| | - Giovanni Biccai
- Regional Environmental Protection Agency of Lombardia, Italy
| | - Pietro Genoni
- Regional Environmental Protection Agency of Lombardia, Italy
| | - Gianluca Corno
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy.
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5
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Sivalingam P, Sabatino R, Sbaffi T, Fontaneto D, Corno G, Di Cesare A. Extracellular DNA includes an important fraction of high-risk antibiotic resistance genes in treated wastewaters. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121325. [PMID: 36828358 DOI: 10.1016/j.envpol.2023.121325] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/04/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Wastewater treatment plants are among the main hotspots for the release of antibiotic resistance genes (ARGs) into the environment. ARGs in treated wastewater can be found in the intracellular DNA (iDNA) and in the extracellular DNA (eDNA). In this study, we investigated the fate and the distribution (either in eDNA or in iDNA) of ARGs in the treated wastewaters pre and post-disinfection by shotgun metagenomics. The richness of the intracellular resistome was found to be higher than the extracellular one. However, the latter included different high risk ARGs. About 11% of the recovered metagenome assembled genomes (MAGs) from the extracted DNA was positive for at least one ARG and, among them, several were positive for more ARGs. The high-risk ARG bacA was the most frequently detected gene among the MAGs. The disinfection demonstrated to be an important driver of the composition of the antibiotic resistomes. Our results demonstrated that eDNA represents an important fraction of the overall ARGs, including a number of high-risk ARGs, which reach the environment with treated wastewater effluents. The studied disinfections only marginally affect the whole antibiotic resistome but cause important shifts from intracellular to extracellular DNA, potentially threating human health.
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Affiliation(s)
- Periyasamy Sivalingam
- National Research Council of Italy - Water Research Institute (CNR-IRSA), Molecular Ecology Group (MEG), Verbania, Italy
| | - Raffaella Sabatino
- National Research Council of Italy - Water Research Institute (CNR-IRSA), Molecular Ecology Group (MEG), Verbania, Italy
| | - Tomasa Sbaffi
- National Research Council of Italy - Water Research Institute (CNR-IRSA), Molecular Ecology Group (MEG), Verbania, Italy
| | - Diego Fontaneto
- National Research Council of Italy - Water Research Institute (CNR-IRSA), Molecular Ecology Group (MEG), Verbania, Italy
| | - Gianluca Corno
- National Research Council of Italy - Water Research Institute (CNR-IRSA), Molecular Ecology Group (MEG), Verbania, Italy.
| | - Andrea Di Cesare
- National Research Council of Italy - Water Research Institute (CNR-IRSA), Molecular Ecology Group (MEG), Verbania, Italy
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Corno G, Ghaly T, Sabatino R, Eckert EM, Galafassi S, Gillings MR, Di Cesare A. Class 1 integron and related antimicrobial resistance gene dynamics along a complex freshwater system affected by different anthropogenic pressures. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120601. [PMID: 36351483 DOI: 10.1016/j.envpol.2022.120601] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/10/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
The risk for human health posed by polluted aquatic environments, and especially those carrying antibiotic resistance genes (ARGs) of clinical interest, is still debated. This is because of our limited knowledge of the dynamics of antimicrobial resistance in the environment, the selection mechanisms underlying the spread of ARGs, and the ecological factors potentially favoring their return to humans. The Class 1 integron is one of the most effective platforms for the dissemination of ARGs. In this study we investigated a freshwater system consisting of a lake-river-lake continuum, determining the abundance of class 1 integrons and their associated ARGs by a modulated metagenomic approach. Bacterial abundance and community composition were used to identify the potential carriers of class 1 integrons and their associated ARGs over a period of six months. Class 1 integrons and their ARG cargoes were significantly more abundant in riverine sampling sites receiving treated wastewater. Further, class 1 integrons carried ARGs ranked at the highest risk for human health (e.g., catB genes), in particular, genes encoding resistance to aminoglycosides. Genera of potential pathogens, such as Pseudomonas and Escherichia-Shigella, were correlated with class 1 integrons. The lake-river-lake system demonstrated a clear relationship between the integrase gene of class 1 integrons (intI1) and anthropogenic impact, but also a strong environmental filtering that favored the elimination of intI1 once the human derived stressors were reduced. Overall, the results of this study underline the role class 1 integrons as proxy of anthropogenic pollution and suggest this genetic platform as an important driver of aminoglycoside resistance genes, including high risk ARGs, of potential concern for human health.
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Affiliation(s)
- Gianluca Corno
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy.
| | - Timothy Ghaly
- ARC Centre of Excellence in Synthetic Biology and Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Raffaella Sabatino
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Ester M Eckert
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Silvia Galafassi
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Michael R Gillings
- ARC Centre of Excellence in Synthetic Biology and Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Andrea Di Cesare
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
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7
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Goodarzi Z, Asad S, Mehrshad M. Genome-resolved insight into the reservoir of antibiotic resistance genes in aquatic microbial community. Sci Rep 2022; 12:21047. [PMID: 36473884 PMCID: PMC9726936 DOI: 10.1038/s41598-022-25026-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
Aquatic microbial communities are an important reservoir of antibiotic resistance genes (ARGs). However, distribution and diversity of different ARG categories in environmental microbes with different ecological strategies is not yet well studied. Despite the potential exposure of the southern part of the Caspian Sea to the release of antibiotics, little is known about its natural resistome profile. We used a combination of Hidden Markov model (HMM), homology alignment and a deep learning approach for comprehensive screening of the diversity and distribution of ARGs in the Caspian Sea metagenomes at genome resolution. Detected ARGs were classified into five antibiotic resistance categories including prevention of access to target (44%), modification/protection of targets (30%), direct modification of antibiotics (22%), stress resistance (3%), and metal resistance (1%). The 102 detected ARG containing metagenome-assembled genomes of the Caspian Sea were dominated by representatives of Acidimicrobiia, Gammaproteobacteria, and Actinobacteria classes. Comparative analysis revealed that the highly abundant, oligotrophic, and genome streamlined representatives of taxa Acidimicrobiia and Actinobacteria modify the antibiotic target via mutation to develop antibiotic resistance rather than carrying extra resistance genes. Our results help with understanding how the encoded resistance categories of each genome are aligned with its ecological strategies.
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Affiliation(s)
- Zahra Goodarzi
- grid.46072.370000 0004 0612 7950Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Sedigheh Asad
- grid.46072.370000 0004 0612 7950Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Maliheh Mehrshad
- grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Box 7050, 75007 Uppsala, Sweden
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Sekizuka T, Tanaka R, Hashino M, Yatsu K, Kuroda M. Comprehensive Genome and Plasmidome Analysis of Antimicrobial Resistant Bacteria in Wastewater Treatment Plant Effluent of Tokyo. Antibiotics (Basel) 2022; 11:antibiotics11101283. [PMID: 36289941 PMCID: PMC9598598 DOI: 10.3390/antibiotics11101283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 01/01/2023] Open
Abstract
To characterize environmental antimicrobial resistance (AMR) in urban areas, extended-spectrum β-lactamase- (ESBL)/carbapenemase-producing bacteria (EPB/CPB, respectively) from urban wastewater treatment plant effluents in Tokyo were isolated on CHROMagar ESBL plate. Complete genome sequence analysis, including plasmids, indicated that 126 CTX-M-positive isolates (31%) were identified among the 404 obtained isolates. The CTX-M-9 group was predominant (n = 65, 52%), followed by the CTX-M-1 group (n = 44, 35%). Comparative genome analysis revealed that CTX-M-27-positive E. coli O16:H5-ST131-fimH41 exhibited a stable genome structure and clonal-global dissemination. Plasmidome network analysis revealed that 304 complete plasmid sequences among 85 isolates were grouped into 14 incompatibility (Inc) network communities (Co1 to Co14). Co10 consisted of primarily IncFIA/IncFIB plasmids harboring blaCTX-M in E. coli, whereas Co12 consisted primarily of IncFIA(HI1)/Inc FIB(K) plasmids harboring blaCTX-M, blaKPC, and blaGES in Klebsiella spp. Co11 was markedly located around Co10 and Co12. Co11 exhibited blaCTX-M, blaKPC, and blaNDM, and was mainly detected in E. coli and Klebsiella spp. from human and animal sources, suggesting a mutual role of Co11 in horizontal gene transfer between E. coli and Klebsiella spp. This comprehensive resistome analysis uncovers the mode of relational transfer among bacterial species, highlighting the potential source of AMR burden on public health in urban communities.
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