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Lin L, Li L, Yang X, Hou L, Wu D, Wang B, Ma B, Liao X, Yan X, Gad M, Su J, Liu Y, Liu K, Hu A. Unnoticed antimicrobial resistance risk in Tibetan cities unveiled by sewage metagenomic surveillance: Compared to the eastern Chinese cities. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135730. [PMID: 39243538 DOI: 10.1016/j.jhazmat.2024.135730] [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: 05/25/2024] [Revised: 08/26/2024] [Accepted: 08/31/2024] [Indexed: 09/09/2024]
Abstract
Sewage surveillance is a cost-effective tool for assessing antimicrobial resistance (AMR) in urban populations. However, research on sewage AMR in remote areas is still limited. Here, we used shotgun metagenomic sequencing to profile antibiotic resistance genes (ARGs) and ARG-carrying pathogens (APs) across 15 cities in Tibetan Plateau (TP) and the major cities in eastern China. Notable regional disparities in sewage ARG composition were found, with a significantly higher ARG abundance in TP (2.97 copies/cell). A total of 542 and 545 APs were identified in sewage from TP and the East, respectively, while more than 40 % carried mobile genetic elements (MGEs). Moreover, 65 MGEs-carrying APs were identified as World Health Organization (WHO) priority-like bacterial and fungal pathogens. Notably, a fungal zoonotic pathogen, Enterocytozoon bieneusi, was found for the first time to carry a nitroimidazole resistance gene (nimJ). Although distinct in AP compositions, the relative abundances of APs were comparable in these two regions. Furthermore, sewage in TP was found to be comparable to the cities in eastern China in terms of ARG mobility and AMR risks. These findings provide insights into ARGs and APs distribution in Chinese sewage and stress the importance of AMR surveillance and management strategies in remote regions.
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Affiliation(s)
- Laichang Lin
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Laiyi Li
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyong Yang
- School of Environmental and Material Engineering, Yantai University, Yantai 264005, China
| | - Liyuan Hou
- Department of Civil and Environmental Engineering, Utah State University, Logan, UT 84322, United States; Utah Water Research Laboratory, 1600 Canyon Road, Logan, UT 84321, United States
| | - Dong Wu
- Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, China
| | - Binhao Wang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bin Ma
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xin Liao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuhang Yan
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Life Sciences, Hebei University, Baoding 071002, China
| | - Mahmoud Gad
- Water Pollution Research Department, National Research Centre, Cairo 12622, Egypt
| | - Jianqiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yongqin Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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2
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Qi Q, Ghaly TM, Rajabal V, Russell DH, Gillings MR, Tetu SG. Vegetable phylloplane microbiomes harbour class 1 integrons in novel bacterial hosts and drive the spread of chlorite resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176348. [PMID: 39304140 DOI: 10.1016/j.scitotenv.2024.176348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 09/10/2024] [Accepted: 09/15/2024] [Indexed: 09/22/2024]
Abstract
Bacterial hosts in vegetable phylloplanes carry mobile genetic elements, such as plasmids and transposons that are associated with integrons. These mobile genetic elements and their cargo genes can enter human microbiomes via consumption of fresh agricultural produce, including uncooked vegetables. This presents a risk of acquiring antimicrobial resistance genes from uncooked vegetables. To better understand horizontal gene transfer of class 1 integrons in these compartments, we applied epicPCR, a single-cell fusion-PCR surveillance technique, to link the class 1 integron integrase (intI1) gene with phylogenetic markers of their bacterial hosts. Ready-to-eat salads carried class 1 integrons from the phyla Bacteroidota and Pseudomonadota, including four novel genera that were previously not known to be associated with intI1. We whole-genome sequenced Pseudomonas and Erwinia hosts of pre-clinical class 1 integrons that are embedded in Tn402-like transposons. The proximal gene cassette in these integrons was identified as a chlorite dismutase gene cassette, which we showed experimentally to confer chlorite resistance. Chlorine-derived compounds such as acidified sodium chlorite and chloride dioxide are used to disinfectant raw vegetables in food processing facilities, suggesting selection for chlorite resistance in phylloplane integrons. The spread of integrons conferring chlorite resistance has the potential to exacerbate integron-mediated antimicrobial resistance (AMR) via co-selection of chlorite resistance and AMR, thus highlighting the importance of monitoring chlorite residues in agricultural produce. These results demonstrate the strength of combining epicPCR and culture-based isolation approaches for identifying hosts and dissecting the molecular ecology of class 1 integrons.
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Affiliation(s)
- Qin Qi
- School of Natural Sciences, Macquarie University, New South Wales, Australia; Manchester Institute of Biotechnology, The University of Manchester, Greater Manchester, United Kingdom.
| | - Timothy M Ghaly
- School of Natural Sciences, Macquarie University, New South Wales, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, New South Wales, Australia; ARC Centre of Excellence for Synthetic Biology, Macquarie University, New South Wales, Australia
| | - Dylan H Russell
- School of Natural Sciences, Macquarie University, New South Wales, Australia
| | - Michael R Gillings
- School of Natural Sciences, Macquarie University, New South Wales, Australia
| | - Sasha G Tetu
- School of Natural Sciences, Macquarie University, New South Wales, Australia; ARC Centre of Excellence for Synthetic Biology, Macquarie University, New South Wales, Australia.
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3
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Tuo J, Shen Y, Jia S, Liu S, Zhang Q, Wang D, He X, Liu P, Zhang XX. HPB-Chip: An accurate high-throughput qPCR-based tool for rapidly profiling waterborne human pathogenic bacteria in the environment. WATER RESEARCH 2024; 260:121927. [PMID: 38941866 DOI: 10.1016/j.watres.2024.121927] [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: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 06/30/2024]
Abstract
Waterborne pathogens are threatening public health globally, but profiling multiple human pathogenic bacteria (HPBs) in various polluted environments is still a challenge due to the absence of rapid, high-throughput and accurate quantification tools. This work developed a novel chip, termed the HPB-Chip, based on high-throughput quantitative polymerase chain reactions (HT-qPCR). The HPB-Chip with 33-nL reaction volume could simultaneously complete 10,752 amplification reactions, quantifying 27 HPBs in up to 192 samples with two technical replicates (including those for generating standard curves). Specific positive bands of target genes across different species and single peak melting curves demonstrated high specificity of the HPB-Chip. The mixed plasmid serial dilution test validated its high sensitivity with the limit of quantification (LoD) of averaged 82 copies per reaction for 25 target genes. PCR amplification efficiencies and R2 coefficients of standard curves of the HPB-Chip averaged 101 % and 0.996, respectively. Moreover, a strong positive correlation (Pearson' r: 0.961-0.994, P < 0.001) of HPB concentrations (log10 copies/L) between HPB-Chip and conventional qPCR demonstrated high accuracy of the HPB-Chip. Subsequently, the HPB-Chip has been successfully applied to absolutely quantify 27 HPBs in municipal and hospital wastewater treatment plants (WWTPs) after PMA treatment. A total of 17 HPBs were detected in the 6 full-scale WWTPs, with an additional 19 in the hospital WWTP. Remarkably, Acinetobacter baumannii, Legionella pneumophila, and Arcobacter butzler were present in the final effluent of each municipal WWTP. Overall, the HPB-Chip is an efficient and accurate high-throughput quantification tool to comprehensively and rapidly quantify 27 HPBs in the environment.
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Affiliation(s)
- Jinhua Tuo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yan Shen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Shuyu Jia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengnan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Qifeng Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Depeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiwei He
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Peng Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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Ma Y, Qiao Y, Zhang X, Ye L. Filamentous bacteria-induced sludge bulking can alter antibiotic resistance gene profiles and increase potential risks in wastewater treatment systems. ENVIRONMENT INTERNATIONAL 2024; 190:108920. [PMID: 39094405 DOI: 10.1016/j.envint.2024.108920] [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: 06/11/2024] [Revised: 07/28/2024] [Accepted: 07/28/2024] [Indexed: 08/04/2024]
Abstract
Sludge bulking caused by filamentous bacteria is a prevalent issue in wastewater treatment systems. While previous studies have primarily concentrated on controlling sludge bulking, the biological risks associated with it have been overlooked. This study demonstrates that excessive growth of filamentous bacteria during sludge bulking can significantly increase the abundance of antibiotic resistance genes (ARGs) in activated sludge. Through metagenomic analysis, we identified specific ARGs carried by filamentous bacteria, such as Sphaerotilus and Thiothrix, which are responsible for bulking. Additionally, by examining over 1,000 filamentous bacterial genomes, we discovered a diverse array of ARGs across different filamentous bacteria derived from wastewater treatment systems. Our findings indicate that 74.84% of the filamentous bacteria harbor at least one ARG, with the occurrence frequency of ARGs in these bacteria being approximately 1.5 times higher than that in the overall bacterial population in activated sludge. Furthermore, genomic and metagenomic analyses have shown that the ARGs in filamentous bacteria are closely linked to mobile genetic elements and are frequently found in potentially pathogenic bacteria, highlighting potential risks posed by these filamentous bacteria. These insights enhance our understanding of ARGs in activated sludge and underscore the importance of risk management in wastewater treatment systems.
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Affiliation(s)
- Yanyan Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Yiheng Qiao
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu, China.
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5
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Bombaywala S, Bajaj A, Dafale NA. Meta-analysis of wastewater microbiome for antibiotic resistance profiling. J Microbiol Methods 2024; 223:106953. [PMID: 38754482 DOI: 10.1016/j.mimet.2024.106953] [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: 03/21/2024] [Revised: 05/12/2024] [Accepted: 05/12/2024] [Indexed: 05/18/2024]
Abstract
The microbial composition and stress molecules are main drivers influencing the development and spread of antibiotic resistance bacteria (ARBs) and genes (ARGs) in the environment. A reliable and rapid method for identifying associations between microbiome composition and resistome remains challenging. In the present study, secondary metagenome data of sewage and hospital wastewaters were assessed for differential taxonomic and ARG profiling. Subsequently, Random Forest (RF)-based ML models were used to predict ARG profiles based on taxonomic composition and model validation on hospital wastewaters. Total ARG abundance was significantly higher in hospital wastewaters (15 ppm) than sewage (5 ppm), while the resistance towards methicillin, carbapenem, and fluoroquinolone were predominant. Although, Pseudomonas constituted major fraction, Streptomyces, Enterobacter, and Klebsiella were characteristic of hospital wastewaters. Prediction modeling showed that the relative abundance of pathogenic genera Escherichia, Vibrio, and Pseudomonas contributed most towards variations in total ARG count. Moreover, the model was able to identify host-specific patterns for contributing taxa and related ARGs with >90% accuracy in predicting the ARG subtype abundance. More than >80% accuracy was obtained for hospital wastewaters, demonstrating that the model can be validly extrapolated to different types of wastewater systems. Findings from the study showed that the ML approach could identify ARG profile based on bacterial composition including 16S rDNA amplicon data, and can serve as a viable alternative to metagenomic binning for identification of potential hosts of ARGs. Overall, this study demonstrates the promising application of ML techniques for predicting the spread of ARGs and provides guidance for early warning of ARBs emergence.
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Affiliation(s)
- Sakina Bombaywala
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Abhay Bajaj
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nishant A Dafale
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Drane K, Sheehan M, Whelan A, Ariel E, Kinobe R. The Role of Wastewater Treatment Plants in Dissemination of Antibiotic Resistance: Source, Measurement, Removal and Risk Assessment. Antibiotics (Basel) 2024; 13:668. [PMID: 39061350 PMCID: PMC11274174 DOI: 10.3390/antibiotics13070668] [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: 06/10/2024] [Revised: 07/05/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Antibiotic Resistance Genes (ARGs) are contaminants of emerging concern with marked potential to impact public and environmental health. This review focusses on factors that influence the presence, abundance, and dissemination of ARGs within Wastewater Treatment Plants (WWTPs) and associated effluents. Antibiotic-Resistant Bacteria (ARB) and ARGs have been detected in the influent and the effluent of WWTPs worldwide. Different levels of wastewater treatment (primary, secondary, and tertiary) show different degrees of removal efficiency of ARGs, with further differences being observed when ARGs are captured as intracellular or extracellular forms. Furthermore, routinely used molecular methodologies such as quantitative polymerase chain reaction or whole genome sequencing may also vary in resistome identification and in quantifying ARG removal efficiencies from WWTP effluents. Additionally, we provide an overview of the One Health risk assessment framework, as well as future strategies on how WWTPs can be assessed for environmental and public health impact.
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Affiliation(s)
- Kezia Drane
- College of Public Health Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
| | - Madoc Sheehan
- College of Science, Technology, and Engineering, James Cook University, Townsville, QLD 4811, Australia;
| | - Anna Whelan
- Townsville Water and Waste, Wastewater Operations, Townsville, QLD 4810, Australia;
| | - Ellen Ariel
- College of Public Health Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
| | - Robert Kinobe
- College of Public Health Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
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Tavares RDS, Fidalgo C, Rodrigues ET, Tacão M, Henriques I. Integron-associated genes are reliable indicators of antibiotic resistance in wastewater despite treatment- and seasonality-driven fluctuations. WATER RESEARCH 2024; 258:121784. [PMID: 38761599 DOI: 10.1016/j.watres.2024.121784] [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: 12/20/2023] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
The present study aims to characterize the bacterial community, resistome and integron abundance of a municipal wastewater treatment plant (WWTP) over the course of 12 months and evaluate the year-long performance of integron-related genes as potential indicators of antibiotic resistance mechanisms in influents and effluents. For that, total DNA was extracted and subjected to 16S rRNA-targeted metabarcoding, high-throughput (HT) qPCR (48 targets) and standard qPCR (5 targets). Targets included integrase genes, antibiotic resistance genes (ARGs) and putative pathogenic groups. A total of 16 physicochemical parameters determined in the wastewater samples were also considered. Results revealed that the WWTP treatment significantly impacted the bacterial community, as well as the content in ARGs and integrase genes. Indeed, there was a relative enrichment from influent to effluent of 13 pathogenic groups (e.g., Legionella and Mycobacterium) and genes conferring resistance to sulphonamides, aminoglycosides and disinfectants. Effluent samples (n = 25) also presented seasonal differences, with an increase of the total ARGs' concentration in summer, and differences between winter and summer on relative abundance of sulphonamide and disinfectant resistance mechanisms. From the eight putative integron-related genes selected, all were positively correlated with the total ARGs' content in wastewater and the relative abundance of resistance to most of the specific antibiotic classes. The genes intI1, blaGES and qacE∆1 were the most strongly correlated with the total concentration of ARGs. Genes blaGES and blaVIM, were better correlated to resistance to beta-lactams, aminoglycosides and tetracyclines. This study supports the use of integron-related genes as powerful indicators of antibiotic resistance in wastewater, being robust despite the variability caused by wastewater treatment and seasonality.
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Affiliation(s)
- Rafael D S Tavares
- Department of Life Sciences, Centre for Functional Ecology, Associate Laboratory TERRA, Faculty of Sciences and Technology, University of Coimbra, 3000-456, Coimbra, Portugal; Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Cátia Fidalgo
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Elsa T Rodrigues
- Department of Life Sciences, Centre for Functional Ecology, Associate Laboratory TERRA, Faculty of Sciences and Technology, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Marta Tacão
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.
| | - Isabel Henriques
- Department of Life Sciences, Centre for Functional Ecology, Associate Laboratory TERRA, Faculty of Sciences and Technology, University of Coimbra, 3000-456, Coimbra, Portugal
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Gillieatt BF, Coleman NV. Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria. FEMS Microbiol Rev 2024; 48:fuae017. [PMID: 38897736 PMCID: PMC11253441 DOI: 10.1093/femsre/fuae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 06/09/2024] [Accepted: 06/18/2024] [Indexed: 06/21/2024] Open
Abstract
The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotics have been proposed, however, the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation has been described but more in-depth characterizations are needed, using methodologies that confirm the functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.
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Affiliation(s)
- Brodie F Gillieatt
- School of Life and Environmental Sciences, The University of Sydney, F22 - LEES Building, NSW 2006, Australia
| | - Nicholas V Coleman
- School of Natural Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, 6 Wally’s Walk, Macquarie Park, NSW 2109, Australia
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9
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Martak D, Henriot CP, Hocquet D. Environment, animals, and food as reservoirs of antibiotic-resistant bacteria for humans: One health or more? Infect Dis Now 2024; 54:104895. [PMID: 38548016 DOI: 10.1016/j.idnow.2024.104895] [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: 11/17/2023] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/15/2024]
Abstract
Antimicrobial resistance (AMR) is a major public health challenge. For several years, AMR has been addressed through a One Health approach that links human health, animal health, and environmental quality. In this review, we discuss AMR in different reservoirs with a focus on the environment. Anthropogenic activities produce effluents (sewage, manure, and industrial wastes) that contaminate soils and aquatic environments with antibiotic-resistant bacteria (ARB), antibiotic-resistant genes (ARGs), and selective agents such as antibiotics, biocides, and heavy metals. Livestock treated with antibiotics can also contaminate food with ARB. In high-income countries (HICs), effective sanitation infrastructure and limited pharmaceutical industries result in more controlled discharges associated with human activities. Hence, studies using genome-based typing methods have revealed that, although rare inter-reservoir transmission events have been reported, human acquisition in HICs occurs primarily through person-to-person transmission. The situation is different in low- and middle-income countries (LMICs) where high population density, poorer sanitation and animal farming practices are more conducive to inter-reservoir transmissions. In addition, environmental bacteria can be a source of ARGs that, when transferred to pathogenic species under antibiotic selection pressure in environmental hotspots, produce new antibiotic-resistant strains that can potentially spread in the human community through human-to-human transmission. The keys to reducing AMR in the environment are (i) better treatment of human waste by improving wastewater treatment plants (WWTPs) in HICs and improving sanitation infrastructure in LMICs, (ii) reducing the use of antibiotics by humans and animals, (iii) prioritizing the use of less environmentally harmful antibiotics, and (iv) better control of pharmaceutical industry waste.
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Affiliation(s)
- Daniel Martak
- Université de Franche-Comté, UMR 6249 Chrono-environnement, F-25000 Besançon, France.
| | - Charles P Henriot
- Université de Franche-Comté, UMR 6249 Chrono-environnement, F-25000 Besançon, France
| | - Didier Hocquet
- Université de Franche-Comté, UMR 6249 Chrono-environnement, F-25000 Besançon, France; CHU de Besançon, Hygiène Hospitalière, F-25000 Besançon, France
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10
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Dekić Rozman S, Puljko A, Karkman A, Virta M, Udiković-Kolić N. Bacterial hosts of clinically significant beta-lactamase genes in Croatian wastewaters. FEMS Microbiol Ecol 2024; 100:fiae081. [PMID: 38796694 PMCID: PMC11165274 DOI: 10.1093/femsec/fiae081] [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: 09/13/2023] [Revised: 05/02/2024] [Accepted: 05/24/2024] [Indexed: 05/28/2024] Open
Abstract
Wastewater treatment plants (WWTPs) provide a suitable environment for the interaction of antibiotic resistant bacteria and antibiotic-resistance genes (ARGs) from human, animal, and environmental sources. The aim was to study the influent and effluent of two WWTPs in Croatia to identify bacterial hosts of clinically important beta-lactamase genes (blaTEM, blaVIM, blaOXA-48-like) and observe how their composition changes during the treatment process. A culture-independent epicPCR (Emulsion, Paired isolation and Concatenation Polymerase Chain Reaction) was used to identify the ARG hosts, and 16S rRNA amplicon sequencing to study the entire bacterial community. Different wastewater sources contributed to the significant differences in bacterial composition of the wastewater between the two WWTPs studied. A total of 167 genera were detected by epicPCR, with the Arcobacter genus, in which all ARGs studied were present, dominating in both WWTPs. In addition, the clinically important genera Acinetobacter and Aeromonas contained all ARGs examined. The blaOXA-48-like gene had the highest number of hosts, followed by blaVIM, while blaTEM had the narrowest host range. Based on 16S rRNA gene sequencing, ARG hosts were detected in both abundant and rare taxa. The number of hosts carrying investigated ARGs was reduced by wastewater treatment. EpicPCR provided valuable insights into the bacterial hosts of horizontally transmissible beta-lactamase genes in Croatian wastewater.
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Affiliation(s)
- Svjetlana Dekić Rozman
- Department of Microbiology, University of Helsinki, Viikinkaari 9 00014 Helsinki, Finland
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54 10 000 Zagreb, Croatia
| | - Ana Puljko
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54 10 000 Zagreb, Croatia
| | - Antti Karkman
- Department of Microbiology, University of Helsinki, Viikinkaari 9 00014 Helsinki, Finland
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Viikinkaari 9 00014 Helsinki, Finland
| | - Nikolina Udiković-Kolić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54 10 000 Zagreb, Croatia
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Lou EG, Fu Y, Wang Q, Treangen TJ, Stadler LB. Sensitivity and consistency of long- and short-read metagenomics and epicPCR for the detection of antibiotic resistance genes and their bacterial hosts in wastewater. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133939. [PMID: 38490149 DOI: 10.1016/j.jhazmat.2024.133939] [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: 07/27/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 03/17/2024]
Abstract
Wastewater surveillance is a powerful tool to assess the risks associated with antibiotic resistance in communities. One challenge is selecting which analytical tool to deploy to measure risk indicators, such as antibiotic resistance genes (ARGs) and their respective bacterial hosts. Although metagenomics is frequently used for analyzing ARGs, few studies have compared the performance of long-read and short-read metagenomics in identifying which bacteria harbor ARGs in wastewater. Furthermore, for ARG host detection, untargeted metagenomics has not been compared to targeted methods such as epicPCR. Here, we 1) evaluated long-read and short-read metagenomics as well as epicPCR for detecting ARG hosts in wastewater, and 2) investigated the host range of ARGs across the wastewater treatment plant (WWTP) to evaluate host proliferation. Results highlighted long-read revealed a wider range of ARG hosts compared to short-read metagenomics. Nonetheless, the ARG host range detected by long-read metagenomics only represented a subset of the hosts detected by epicPCR. The ARG-host linkages across the influent and effluent of the WWTP were characterized. Results showed the ARG-host phylum linkages were relatively consistent across the WWTP, whereas new ARG-host species linkages appeared in the WWTP effluent. The ARG-host linkages of several clinically relevant species found in the effluent were identified.
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Affiliation(s)
- Esther G Lou
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Yilei Fu
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Qi Wang
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA.
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12
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Wang L, Chen M, Wu Y, Chen X, Jin H, Huang J. Spatial distribution and vertical characteristics of microplastics in the urban river: The case of Qinhuai River in Nanjing, China. MARINE POLLUTION BULLETIN 2024; 199:115973. [PMID: 38171161 DOI: 10.1016/j.marpolbul.2023.115973] [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: 10/18/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
Microplastics (MPs) are emerging as global environmental pollutants, significantly influencing the safety of city rivers. This study investigated six sampling sites in the Qinhuai River of Nanjing, which explored the distribution and characteristics of MPs and the microbial structure in 2023. The studied river contained various levels of MPs with average concentrations of 667.68 items/L, whose abundance firstly decreased midstream and then increased downstream. The MPs abundance upstream was higher in surface water column, microplastics midstream and downstream accumulated more in deep water column. Black and blue are prevalent in the color distribution, while the polymers of PC, PP and PS changed with increasing depth, with a proportion of 74 % ∼ 97 % in the dominant shapes of granules. Furthermore, the water with higher MPs may stimulate the growth of MPs-related bacteria in sediments, including the genus of Pseudoxanthomonas and Dechloromonas. Our research will provide constructive support for enhancing urban river management strategies.
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Affiliation(s)
- Luming Wang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing 210096, China
| | - Ming Chen
- Nanjing Research Institute of Environmental Protection, Nanjing 210008, China
| | - Yufeng Wu
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing 210096, China
| | - Xuan Chen
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing 210096, China
| | - Hui Jin
- Nanjing Research Institute of Environmental Protection, Nanjing 210008, China
| | - Juan Huang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing 210096, China.
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13
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Heljanko V, Tyni O, Johansson V, Virtanen JP, Räisänen K, Lehto KM, Lipponen A, Oikarinen S, Pitkänen T, Heikinheimo A. Clinically relevant sequence types of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae detected in Finnish wastewater in 2021-2022. Antimicrob Resist Infect Control 2024; 13:14. [PMID: 38291521 PMCID: PMC10829384 DOI: 10.1186/s13756-024-01370-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/22/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a critical threat to human health. Escherichia coli and Klebsiella pneumoniae are clinically the most important species associated with AMR and are the most common carbapenemase-producing (CP) Enterobacterales detected in human specimens in Finland. Wastewater surveillance has emerged as a potential approach for population-level surveillance of AMR, as wastewater could offer a reflection from a larger population with one sample and minimal recognized ethical issues. In this study, we investigated the potential of wastewater surveillance to detect CP E. coli and K. pneumoniae strains similar to those detected in human specimens. METHODS Altogether, 89 composite samples of untreated community wastewater were collected from 10 wastewater treatment plants across Finland in 2021-2022. CP E. coli and K. pneumoniae were isolated using selective culture media and identified using MALDI-TOF MS. Antimicrobial susceptibility testing was performed using disk diffusion test and broth microdilution method, and a subset of isolates was characterized using whole-genome sequencing. RESULTS CP E. coli was detected in 26 (29.2%) and K. pneumoniae in 25 (28.1%) samples. Among E. coli, the most common sequence type (ST) was ST410 (n = 7/26, 26.9%), while ST359 (n = 4/25, 16.0%) predominated among K. pneumoniae. Globally successful STs were detected in both E. coli (ST410, ST1284, ST167, and ST405) and K. pneumoniae (ST512, ST101, and ST307). K. pneumoniae carbapenemases (KPC) were the most common carbapenemases in both E. coli (n = 11/26, 42.3%) and K. pneumoniae (n = 13/25, 52.0%), yet also other carbapenemases, such as blaNDM-5, blaOXA-48, and blaOXA-181, were detected. We detected isolates harboring similar ST and enzyme type combinations previously linked to clusters in Finland, such as E. coli ST410 with blaKPC-2 and K. pneumoniae ST512 with blaKPC-3. CONCLUSIONS Our study highlights the presence of clinically relevant strains of CP E. coli and K. pneumoniae in community wastewater. The results indicate that wastewater surveillance could serve as a monitoring tool for CP Enterobacterales. However, the specificity and sensitivity of the methods should be improved, and technologies, like advanced sequencing methods, should be utilized to distinguish data with public health relevance, harness the full potential of wastewater surveillance, and implement the data in public health surveillance.
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Affiliation(s)
- Viivi Heljanko
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
| | - Olga Tyni
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Venla Johansson
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | - Kati Räisänen
- Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Kirsi-Maarit Lehto
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anssi Lipponen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Tarja Pitkänen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Finnish Food Authority, Seinäjoki, Finland
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14
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Ochman H, Quandt EM, Gottell N, Gilbert JA. Examining the taxonomic distribution of tetracycline resistance in a wastewater plant. SUSTAINABLE MICROBIOLOGY 2024; 1:qvad003. [PMID: 38317688 PMCID: PMC10840452 DOI: 10.1093/sumbio/qvad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/15/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024]
Abstract
Microbial communities serve as reservoirs of antibiotic resistance genes (ARGs) and facilitate the dissemination of these genes to bacteria that infect humans. Relatively little is known about the taxonomic distribution of bacteria harboring ARGs in these reservoirs and the avenues of transmission due to the technical hurdles associated with characterizing the contents of complex microbial populations and the assignment of genes to particular genomes. Focusing on the array of tetracycline resistance (Tcr) genes in the primary and secondary phases of wastewater treatment, 17 of the 22 assayed Tcr genes were detected in at least one sample. We then applied emulsion, paired isolation, and concatenation PCR (epicPCR) to link tetracycline resistance genes to specific bacterial hosts. Whereas Tcr genes tend to vary in their distributions among bacterial taxa according to their modes of action, there were numerous instances in which a particular Tcr gene was associated with a host that was distantly related to all other bacteria bearing the same gene, including several hosts not previously identified. Tcr genes are far less host-restricted than previously assumed, indicating that complex microbial communities serve as settings where ARGs are spread among divergent bacterial phyla.
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Affiliation(s)
- Howard Ochman
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, United States
| | - Erik M Quandt
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, United States
| | - Neil Gottell
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
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15
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Liu CHM, Dahms HU, Hsieh CY, Lin ZY, Lin TY, Huang XQ. Bacterial heavy metal resistance related to environmental conditions. CHEMOSPHERE 2024; 347:140539. [PMID: 37951402 DOI: 10.1016/j.chemosphere.2023.140539] [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: 08/22/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023]
Abstract
Contaminated water bodies such as rivers provide reservoirs for bacterial resistance. This field study tested the water quality and the bacterial resistance to heavy metals of Qishan River water pollution. Wastewater discharged to environmental surface waters is a major pathway of heavy metals and heavy metal-resistant bacteria. Contaminated water bodies such as rivers provide reservoirs for bacterial resistance. This field study tested the water quality and bacterial resistance to heavy metals of Qishan River water pollution. Guided by our research hypothesis that an overall increase in downstream heavy metal resistance levels was following an increase in human settlements were eight sites sampled along the Qishan River. These were situated upstream and downstream to the confluence of the Qishan River with the Kaoping River. In the laboratory bacterial heavy metal resistance was bio-assayed by disk diffusion and micro-dilution with six widely used heavy metals. The comparison of bacterial resistance was among Qishan River upstream sites (sites 1-6) and downstream sites (sites 7-9). Multi-drug-resistant bacteria and co-resistance against heavy metals and antibacterials appeared at site 8. This research discusses the correlation between environmental factors, and antibacterial and heavy metal resistance. The results provide stakeholders and authorities responsible for environmental pollution with a reference for risk assessment and management of bacterial resistance.
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Affiliation(s)
- Cheng-Han Michael Liu
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC; Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC; University Social Responsibility Project Team, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC; Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC; University Social Responsibility Project Team, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC; Department of Marine Biotechnology and Resources, College of Marine Sciences, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan, ROC; Department of Environmental Science and Engineering, College of Engineering, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan, ROC.
| | - Chi-Ying Hsieh
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC; Department of Environmental Science and Engineering, College of Engineering, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan, ROC; Water Resources Education and Research Center, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan, ROC.
| | - Zong-Ying Lin
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC; University Social Responsibility Project Team, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC
| | - Tai-Yan Lin
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC; University Social Responsibility Project Team, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC
| | - Xiao-Qian Huang
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC
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16
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Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 2024; 17:e14408. [PMID: 38226780 PMCID: PMC10832538 DOI: 10.1111/1751-7915.14408] [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: 06/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
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Affiliation(s)
- Maho Tokuda
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityHamamatsuJapan
- Japan Collection of MicroorganismsRIKEN BioResource Research CenterIbarakiJapan
- Graduate School of Integrated Science and TechnologyShizuoka UniversityHamamatsuJapan
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17
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Xu M, Gao P, Chen HQ, Shen XX, Xu RZ, Cao JS. Metagenomic insight into the prevalence and driving forces of antibiotic resistance genes in the whole process of three full-scale wastewater treatment plants. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118369. [PMID: 37356328 DOI: 10.1016/j.jenvman.2023.118369] [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: 03/03/2023] [Revised: 05/17/2023] [Accepted: 06/08/2023] [Indexed: 06/27/2023]
Abstract
The spread of antibiotic resistance genes (ARGs) is an emerging global health concern, and wastewater treatment plants (WWTPs), as an essential carrier for the occurrence and transmission of ARGs, deserves more attention. Based on the Illumina NovaSeq high-throughput sequencing platform, this study conducted a metagenomic analysis of 18 samples from three full-scale WWTPs to explore the fate of ARGs in the whole process (influent, biochemical treatment, advanced treatment, and effluent) of wastewater treatment. Total 70 ARG subtypes were detected, among which multidrug, aminoglycoside, tetracycline, and macrolide ARGs were most abundant. The different treatment processes used for three WWTPs were capable of reducing ARG diversity, but did not significantly reduce ARG abundance. Compared to that by denitrification filters, the membrane bioreactor (MBR) process was advantageous in controlling the prevalence of multidrug ARGs in WWTPs. Linear discriminant analysis Effect Size (LEfSe) suggested g_Nitrospira, g_Curvibacter, and g_Mycobacterium as the key bacteria responsible for differential ARG prevalence among different WWTPs. Meanwhile, adeF, sul1, and mtrA were the persistent antibiotic resistance genes (PARGs) and played dominant roles in the prevalence of ARGs. Proteobacteria and Actinobacteria were the host bacteria of majority ARGs in WWTPs, while Pseudomonas and Nitrospira were the most crucial host bacteria influencing the dissemination of critical ARGs (e.g., adeF). In addition, microbial richness was determined to be the decisive factor affecting the diversity and abundance of ARGs in wastewater treatment processes. Overall, regulating the abundance of microorganisms and key host bacteria by selecting processes with microbial interception, such as MBR process, may be beneficial to control the prevalence of ARGs in WWTPs.
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Affiliation(s)
- Ming Xu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China
| | - Peng Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China
| | - Hao-Qiang Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China
| | - Xiao-Xiao Shen
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.
| | - Run-Ze Xu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China
| | - Jia-Shun Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; College of Environment, Hohai University, Nanjing, 210098, China
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18
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Haenelt S, Richnow HH, Müller JA, Musat N. Antibiotic resistance indicator genes in biofilm and planktonic microbial communities after wastewater discharge. Front Microbiol 2023; 14:1252870. [PMID: 37731921 PMCID: PMC10507703 DOI: 10.3389/fmicb.2023.1252870] [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: 07/04/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023] Open
Abstract
The spread of bacteria with antibiotic resistance genes (ARGs) in aquatic ecosystems is of growing concern as this can pose a risk of transmission to humans and animals. While the impact of wastewater treatment plant (WWTP) effluent on ARG abundance in surface waters has been studied extensively, less is known about the fate of ARGs in biofilms. The proximity and dense growth of microorganisms in combination with the accumulation of higher antibiotic concentrations in biofilms might render biofilms a reservoir for ARGs. Seasonal parameters such as water temperature, precipitation, and antibiotic concentrations should be considered as well, as they may further influence the fate of ARGs in aquatic ecosystems. Here we investigated the effect of WWTP effluent on the abundance of the sulfonamide resistance genes sul1 and sul2, and the integrase gene intI1 in biofilm and surface water compartments of a river in Germany with a gradient of anthropogenic impact using quantitative PCR. Furthermore, we analyzed the bacterial community structure in both compartments via 16S rRNA gene amplicon sequencing, following the river downstream. Additionally, conventional water parameters and sulfonamide concentrations were measured, and seasonal aspects were considered by comparing the fate of ARGs and bacterial community diversity in the surface water compartment between the summer and winter season. Our results show that biofilm compartments near the WWTP had a higher relative abundance of ARGs (up to 4.7%) than surface waters (<2.8%). Sulfonamide resistance genes were more persistent further downstream (>10 km) of the WWTP in the hot and dry summer season than in winter. This finding is likely a consequence of the higher proportion of wastewater and thus wastewater-derived microorganisms in the river during summer periods. We observed distinct bacterial communities and ARG abundance between the biofilm and surface water compartment, but even greater variations when considering seasonal and spatiotemporal parameters. This underscores the need to consider seasonal aspects when studying the fate of ARGs in aquatic ecosystems.
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Affiliation(s)
- Sarah Haenelt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jochen A. Müller
- Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
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19
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Bengtsson-Palme J, Abramova A, Berendonk TU, Coelho LP, Forslund SK, Gschwind R, Heikinheimo A, Jarquín-Díaz VH, Khan AA, Klümper U, Löber U, Nekoro M, Osińska AD, Ugarcina Perovic S, Pitkänen T, Rødland EK, Ruppé E, Wasteson Y, Wester AL, Zahra R. Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs? ENVIRONMENT INTERNATIONAL 2023; 178:108089. [PMID: 37441817 DOI: 10.1016/j.envint.2023.108089] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Antimicrobial resistance (AMR) is a global threat to human and animal health and well-being. To understand AMR dynamics, it is important to monitor resistant bacteria and resistance genes in all relevant settings. However, while monitoring of AMR has been implemented in clinical and veterinary settings, comprehensive monitoring of AMR in the environment is almost completely lacking. Yet, the environmental dimension of AMR is critical for understanding the dissemination routes and selection of resistant microorganisms, as well as the human health risks related to environmental AMR. Here, we outline important knowledge gaps that impede implementation of environmental AMR monitoring. These include lack of knowledge of the 'normal' background levels of environmental AMR, definition of high-risk environments for transmission, and a poor understanding of the concentrations of antibiotics and other chemical agents that promote resistance selection. Furthermore, there is a lack of methods to detect resistance genes that are not already circulating among pathogens. We conclude that these knowledge gaps need to be addressed before routine monitoring for AMR in the environment can be implemented on a large scale. Yet, AMR monitoring data bridging different sectors is needed in order to fill these knowledge gaps, which means that some level of national, regional and global AMR surveillance in the environment must happen even without all scientific questions answered. With the possibilities opened up by rapidly advancing technologies, it is time to fill these knowledge gaps. Doing so will allow for specific actions against environmental AMR development and spread to pathogens and thereby safeguard the health and wellbeing of humans and animals.
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Affiliation(s)
- Johan Bengtsson-Palme
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) in Gothenburg, Sweden.
| | - Anna Abramova
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) in Gothenburg, Sweden
| | - Thomas U Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Zellescher Weg 40, 01217 Dresden, Germany
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rémi Gschwind
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME F-75018 Paris, France
| | - Annamari Heikinheimo
- University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O.Box 66, FI-00014, Finland; Finnish Food Authority, P.O.Box 100, 00027 Seinäjoki, Finland
| | - Víctor Hugo Jarquín-Díaz
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Ayaz Ali Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Department of Biotechnology, University of Malakand, Chakdara, Dir (Lower), Khyber Pakhtunkhwa, Pakistan
| | - Uli Klümper
- Institute of Hydrobiology, Technische Universität Dresden, Zellescher Weg 40, 01217 Dresden, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Marmar Nekoro
- Swedish Knowledge Centre on Pharmaceuticals in the Environment, Swedish Medical Products Agency, P.O Box 26, 751 03 Uppsala, Sweden
| | - Adriana D Osińska
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, P.O.Box 5003 NMBU, N-1432 Ås, Norway
| | - Svetlana Ugarcina Perovic
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Tarja Pitkänen
- University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O.Box 66, FI-00014, Finland; Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O.Box 95, FI-70701 Kuopio, Finland
| | | | - Etienne Ruppé
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME F-75018 Paris, France
| | - Yngvild Wasteson
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, P.O.Box 5003 NMBU, N-1432 Ås, Norway
| | | | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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Ovis-Sánchez JO, Perera-Pérez VD, Buitrón G, Quintela-Baluja M, Graham DW, Morales-Espinosa R, Carrillo-Reyes J. Exploring resistomes and microbiomes in pilot-scale microalgae-bacteria wastewater treatment systems for use in low-resource settings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163545. [PMID: 37080313 DOI: 10.1016/j.scitotenv.2023.163545] [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: 09/30/2022] [Revised: 02/17/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Antibiotic resistance genes (ARGs) released into the environment are an emerging human and environmental health concern, including ARGs spread in wastewater treatment effluents. In low-to-middle income countries (LMICs), an alternate wastewater treatment option instead of conventional systems are low-energy, high-rate algal ponds (HRAP) that use microalgae-bacteria aggregates (MABA) for waste degradation. Here we studied the robustness of ARG removal in MABA-based pilot-scale outdoor systems for 140 days of continuous operation. The HRAP system successfully removed 73 to 88 % chemical oxygen demand and up to 97.4 % ammonia, with aggregate size increasing over operating time. Fourteen ARG classes were identified in the HRAP influent, MABA, and effluent using metagenomics, with the HRAP process reducing total ARG abundances by up to 5-fold from influent to effluent. Parallel qPCR analyses showed the HRAP system significantly reduced exemplar ARGs (p < 0.05), with 1.2 to 4.9, 2.7 to 6.3, 0 to 1.5, and 1.2 to 4.8 log-removals for sul1, tetQ, blaKPC, and intl1 genes, respectively. Sequencing of influent, effluent and MABAs samples showed associated microbial communities differed significantly, with influent communities by Enterobacteriales (clinically relevant ARGs carrying bacteria), which were less evident in MABA and effluent. In this sense, such bacteria might be excluded from MABA due to their good settling properties and the presence of antimicrobial peptides. Microalgae-bacteria treatment systems steadily reduced ARGs from wastewater during operation time, using sunlight as the energetic driver, making them ideal for use in LMIC wastewater treatment applications.
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Affiliation(s)
- Julián O Ovis-Sánchez
- Laboratorio de Investigación en Procesos Avanzados de Tratamiento de Aguas, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Querétaro 76230, Mexico
| | - Victor D Perera-Pérez
- Laboratorio de Investigación en Procesos Avanzados de Tratamiento de Aguas, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Querétaro 76230, Mexico
| | - Germán Buitrón
- Laboratorio de Investigación en Procesos Avanzados de Tratamiento de Aguas, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Querétaro 76230, Mexico
| | - Marcos Quintela-Baluja
- School of Engineering, Newcastle University, Cassie Building, Newcastle upon Tyne NE1 7RU, UK
| | - David W Graham
- School of Engineering, Newcastle University, Cassie Building, Newcastle upon Tyne NE1 7RU, UK
| | - Rosario Morales-Espinosa
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Julián Carrillo-Reyes
- Laboratorio de Investigación en Procesos Avanzados de Tratamiento de Aguas, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Querétaro 76230, Mexico.
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Usman Qamar M, Aatika. Impact of climate change on antimicrobial resistance dynamics: an emerging One Health challenge. Future Microbiol 2023; 18:535-539. [PMID: 37347210 DOI: 10.2217/fmb-2023-0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023] Open
Affiliation(s)
- Muhammad Usman Qamar
- Institute of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, 38000, Pakistan
| | - Aatika
- Institute of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, 38000, Pakistan
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Dai S, He Q, Han Z, Shen W, Deng Y, Wang Y, Qiao W, Yang M, Zhang Y. Uncovering the diverse hosts of tigecycline resistance gene tet(X4) in anaerobic digestion systems treating swine manure by epicPCR. WATER RESEARCH X 2023; 19:100174. [PMID: 36915394 PMCID: PMC10006855 DOI: 10.1016/j.wroa.2023.100174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 06/01/2023]
Abstract
The tet(X4) gene is a clinically important tigecycline resistance gene and has shown high persistence in livestock-related environments. However, the bacterial hosts of tet(X4) remain unknown due to the lack of appropriate approaches. Herein, a culture-independent and high-throughput epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction) method was developed, optimized, and demonstrated for the identification of bacterial hosts carrying tet(X4) from environmental samples. Considering the high sequence similarity between tet(X4) and other tet(X)-variant genes, specific primers and amplification conditions were screened and optimized to identify tet(X4) accurately and link tet(X4) with the 16S rRNA gene, which were further validated using artificially constructed bacterial communities. The epicPCR targeting tet(X4) was applied for the identification of bacterial hosts carrying this resistance gene in anaerobic digestion systems treating swine manure. A total of 19 genera were identified as tet(X4) hosts, which were distributed in the phyla Proteobacteria, Bacteroidota, Firmicutes, and Caldatribacteriota. Sixteen genera and two phyla that were identified have not been previously reported as tet(X4) bacterial hosts. The results indicated that a far more diverse range of bacteria was involved in harboring tet(X4) than previously realized. Compared with the tet(X4) hosts determined by correlation-based network analysis and metagenomic binning, epicPCR revealed a high diversity of tet(X4) hosts even at the phylum level. The epicPCR method developed in this study could be effectively employed to reveal the presence of tet(X4) bacterial hosts from a holistic viewpoint.
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Affiliation(s)
- Shiting Dai
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing He
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenli Shen
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Wei Qiao
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Shi B, Zhao R, Su G, Liu B, Liu W, Xu J, Li Q, Meng J. Metagenomic surveillance of antibiotic resistome in influent and effluent of wastewater treatment plants located on the Qinghai-Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 870:162031. [PMID: 36740063 DOI: 10.1016/j.scitotenv.2023.162031] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
As hotspots for the dissemination of antibiotic resistance genes (ARGs), wastewater treatment plants (WWTPs) have attracted global attention. However, there lacks a sufficient metagenomic surveillance of antibiotic resistome in the WWTPs located on the Qinghai-Tibet Plateau. Here, metagenomic approaches were used to comprehensively investigate the occurrence, mobility potential, and bacterial hosts of ARGs in influent and effluent of 18 WWTPs located on the Qinghai-Tibet Plateau. The total ARG relative abundances and diversity were significantly decreased from influent to effluent across the WWTPs. Multidrug, bacitracin, sulfonamide, aminoglycoside, and beta-lactam ARGs generally consisted of the main ARG types in effluent samples, which were distinct from influent samples. A group of 72 core ARGs accounting for 61.8-95.8 % of the total ARG abundances were shared by all samples. Clinically relevant ARGs mainly conferring resistance to beta-lactams were detected in influent (277 ARGs) and effluent (178 ARGs). Metagenomic assembly revealed that the genetic location of an ARG on a plasmid or a chromosome was related to its corresponding ARG type, demonstrating the distinction in the mobility potential of different ARG types. The abundance of plasmid-mediated ARGs accounted for a much higher proportion than that of chromosome-mediated ARGs in both influent and effluent. Moreover, the ARGs co-occurring with diverse mobile genetic elements in the effluent exhibited a comparable mobility potential with the influent. Furthermore, 137 metagenome-assembled genomes (MAGs) assigned to 13 bacterial phyla were identified as the ARG hosts, which could be effectively treated in most WWTPs. Notably, 46 MAGs were found to carry multiple ARG types and the potential pathogens frequently exhibited multi-antibiotic resistance. Some ARG types tended to be carried by certain bacteria, showing a specific host-resistance association pattern. This study highlights the necessity for metagenomic surveillance and will facilitate risk assessment and control of antibiotic resistome in WWTPs located on the vulnerable area.
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Affiliation(s)
- Bin Shi
- Key Laboratory of Environmental Nanotechnology and Health Effects Research, Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Renxin Zhao
- School of Life Sciences, Central China Normal University, Wuhan 430079, China.
| | - Guijin Su
- Key Laboratory of Environmental Nanotechnology and Health Effects Research, Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bingyue Liu
- School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Wenxiu Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Center for Environmental Health Risk Assessment and Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jian Xu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Center for Environmental Health Risk Assessment and Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Qianqian Li
- Key Laboratory of Environmental Nanotechnology and Health Effects Research, Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Meng
- Key Laboratory of Environmental Nanotechnology and Health Effects Research, Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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Liu CH, Chuang YL, Gurunathan R, Hsieh CY, Dahms HU. Riverine antibacterial resistance gradient determined by environmental factors. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:53685-53701. [PMID: 36864342 DOI: 10.1007/s11356-023-25529-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/19/2023] [Indexed: 06/19/2023]
Abstract
Polluted waterbodies such as rivers provide a pathway or reservoir for bacterial resistance. We studied water quality and bacterial antibacterial resistance along the subtropical Qishan River in Taiwan as a case study of environmental resistance spread in a pristine rural area. Human settlement densities increased generally from pristine mountain sites to the more polluted lowlands. Accordingly, as a working hypothesis, we expected the antibacterial resistance level to increase downstream. We collected sediment samples from 8 stations along the Qishan river and where the Qishan river reaches the Kaoping river. The samples were processed in the lab for bacteriological and physicochemical analysis. Antibacterial resistance was tested with common antibacterial. A comparison was made among the sites where isolates began to occur at the upstream (sites 1-6) with the downstream, including site 7 (Qishan town), site 8 (wastewater treatment plant), and site 9 (Kaoping river). The results of multivariate analysis for bacteriological and physicochemical parameters showed increasing water pollution levels downstream of the Qishan river. Bacterial isolates including Escherichia coli, Klebsiella pneumoniae, Serratia marcescens, Enterobacter sp., Acinetobacter sp., Staphylococcus spp., and Bacillus spp. were analyzed and tested in the study. Their percentage of occurrence varied at each site. The resistance level was determined from the growth inhibition zone diameter (disk diffusion) and the minimum inhibitory concentration (micro-dilution). The results indicated that antibacterial resistance was related to certain environmental factors. Besides, the usage pattern of different classes of antibacterial in different sections could alter trends of their resistance. Bacteria were found with increased resistance to antibacterial used in agriculture through the downstream sites. The WWTP discharging wastewater was demonstrated to be a hotspot of resistance in aquatic environments. In conclusion, bacterial resistance against antibacterial from the Qishan river has become a potential public health threat. This study could assist authorities by providing a reference for risk assessment and management of water quality in Kaohsiung city and southern Taiwan.
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Affiliation(s)
- Cheng-Han Liu
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, Republic of China
- University Social Responsibility Team, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, Republic of China
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, Republic of China
| | - Yi-Lynne Chuang
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, Republic of China
| | - Revathi Gurunathan
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, Republic of China
- Department of Medicinal and Applied Chemistry, College of Life Science, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, Republic of China
| | - Chi-Ying Hsieh
- Department of Environmental Science and Engineering, College of Engineering, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan, Republic of China.
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, Republic of China.
- University Social Responsibility Team, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, Republic of China.
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, Republic of China.
- Department of Marine Biotechnology and Resources, College of Marine Sciences, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan, Republic of China.
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Qi Q, Ghaly TM, Penesyan A, Rajabal V, Stacey JA, Tetu SG, Gillings MR. Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4870-4879. [PMID: 36912846 DOI: 10.1021/acs.est.2c09739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.
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Affiliation(s)
- Qin Qi
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Timothy M Ghaly
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Jeremy Ac Stacey
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Sasha G Tetu
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Michael R Gillings
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
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26
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Huang J, He P, Duan H, Yang Z, Zhang H, Lü F. Leaching risk of antibiotic resistance contamination from organic waste compost in rural areas. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 320:121108. [PMID: 36669719 DOI: 10.1016/j.envpol.2023.121108] [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: 11/03/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
Composting is an important decentralized technology for treating multiple biodegradable organic wastes in rural areas. However, compared to industrial composting (i.e., time and temperature protocols), rural composting is less well-controlled, and the risk of antibiotic resistance genes (ARGs) in these composts needs to be determined. We performed a quantitative determination of ARGs and both prokaryotes and eukaryotes to investigate the liquid-solid leaching ratio and the relationship between ARGs and microbial communities in solid and water extracts of composts collected from rural areas. We observed a high level of sulfonamides resistance genes and tetracyclines resistance genes (10-4-10-2 copies/16S copies). Tet-C and tet-X show the strongest leaching potential in rural organic waste composts with complex hosts in solid and liquid phases. This study showed high ARG abundances in compost solid and water extracts, highlighting the leaching risk of compost ARGs when exposed to runoff or groundwater during open storage and field application.
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Affiliation(s)
- Jinghua Huang
- State Key Laboratory of Pollution Control and Resources Reuse, Tongji University, Shanghai, 200092, PR China; Institute of Waste Treatment & Reclamation, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China
| | - Pinjing He
- State Key Laboratory of Pollution Control and Resources Reuse, Tongji University, Shanghai, 200092, PR China
| | - Haowen Duan
- State Key Laboratory of Pollution Control and Resources Reuse, Tongji University, Shanghai, 200092, PR China
| | - Zhan Yang
- State Key Laboratory of Pollution Control and Resources Reuse, Tongji University, Shanghai, 200092, PR China
| | - Hua Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, Tongji University, Shanghai, 200092, PR China; Institute of Waste Treatment & Reclamation, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, PR China
| | - Fan Lü
- State Key Laboratory of Pollution Control and Resources Reuse, Tongji University, Shanghai, 200092, PR China; Institute of Waste Treatment & Reclamation, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, PR China.
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Oliveira M, Truchado P, Cordero-García R, Gil MI, Soler MA, Rancaño A, García F, Álvarez-Ordóñez A, Allende A. Surveillance on ESBL- Escherichia coli and Indicator ARG in Wastewater and Reclaimed Water of Four Regions of Spain: Impact of Different Disinfection Treatments. Antibiotics (Basel) 2023; 12:antibiotics12020400. [PMID: 36830310 PMCID: PMC9952245 DOI: 10.3390/antibiotics12020400] [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: 01/26/2023] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
In the present study, the occurrence of indicator antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) both in the influent and the effluent of four Spanish wastewater treatment plants (WWTPs) was monitored for 12 months, and the susceptibility profiles of 89 recovered extended spectrum β-lactamase (ESBL)-producing Escherichia coli isolates were obtained against a wide range of antimicrobials. The aim of the study was to better understand whether the current wastewater treatment practices allow us to obtain safe reclaimed water mitigating the spread of ARB and ARGs to the environment. Results showed high concentrations of ESBL-producing E. coli as well as a high prevalence of a range of ARGs in the influent samples. The reclamation treatments implemented in the WWTPs were effective in reducing both the occurrence of ESBL E. coli and ARGs, although significant differences were observed among WWTPs. Despite these reductions in occurrence observed upon wastewater treatment, our findings suggest that WWTP effluents may represent an important source of ARGs, which could be transferred among environmental bacteria and disseminate antimicrobial resistance through the food chain. Remarkably, no major differences were observed in the susceptibility profiles of the ESBL E. coli isolated from influent and effluent waters, indicating that water treatments do not give rise to the emergence of new resistance phenotypes.
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Affiliation(s)
- Márcia Oliveira
- Department of Food Hygiene and Technology, Universidad de León, 24071 León, Spain
- Correspondence: ; Tel.: +34-987291182
| | - Pilar Truchado
- Research Group on Microbiology and Quality of Fruit and Vegetables, Food Science and Technology Department, CEBAS-CSIC, 25, Espinardo, 30100 Murcia, Spain
| | | | - María I. Gil
- Research Group on Microbiology and Quality of Fruit and Vegetables, Food Science and Technology Department, CEBAS-CSIC, 25, Espinardo, 30100 Murcia, Spain
| | - Manuel Abellán Soler
- Entidad Regional de Saneamiento y Depuración de Murcia (ESAMUR), Avda. Juan Carlos I, s/n. Ed. Torre Jemeca, 30009 Murcia, Spain
| | - Amador Rancaño
- Acciona Agua, S.A.U., Avda. de Europa, 18, Parque Empresarial La Moraleja, 28108 Alcobendas, Spain
| | - Francisca García
- Acciona Agua, S.A.U., Avda. de Europa, 18, Parque Empresarial La Moraleja, 28108 Alcobendas, Spain
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, 24071 León, Spain
- Institute of Food Science and Technology, Universidad de León, 24007 León, Spain
| | - Ana Allende
- Research Group on Microbiology and Quality of Fruit and Vegetables, Food Science and Technology Department, CEBAS-CSIC, 25, Espinardo, 30100 Murcia, Spain
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Raza S, Kang KH, Shin J, Shin SG, Chun J, Cho HU, Shin J, Kim YM. Variations in antibiotic resistance genes and microbial community in sludges passing through biological nutrient removal and anaerobic digestion processes in municipal wastewater treatment plants. CHEMOSPHERE 2023; 313:137362. [PMID: 36427585 DOI: 10.1016/j.chemosphere.2022.137362] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Antimicrobial resistance (AMR) represents a relentless, silent pandemic. Contributing to this are wastewater treatment plants (WWTPs), a potential source of antibiotic resistance genes' (ARGs) transmission to the environment, threatening public health. The presence of ARGs in pathogenic bacteria and their release into the environment by WWTPs threatens the public health. The current study investigated changes in ARGs' abundance in biological nutrient removal (BNR) processes and anaerobic digestion (AD) reactors of two WWTPs. Also, microbial community structure, which is known to shape the distribution and abundance of ARGs, was also analyzed. The relative abundance of eight ARGs (tetX, tetA, tetM, TEM, sul1, sul2, ermB and qnrD) was quantified as ARGs' copies/16 S rRNA gene copies using quantitative polymerase chain reaction (qPCR). Microbial community composition was assessed by 16 S rRNA microbiome sequencing analysis. TetX was prevalent among the eight ARGs, followed by TEM and sul1. However, its abundance was decreased in the AD sludges compared to BNR sludges. Proteobacteria was the major bacterial phylum found in all the sludge samples, while Arcobacter, 12up and Acidovorax were the predominant genera. Acinetobacter and Flavobacterium were significantly more abundant in the BNR sludges, while 12up and Aeromonas were predominant in AD sludges. Principal component analysis (PCA) revealed a clear difference in dominant ARGs and bacteria between the sludges in the processes of BNR and AD of the two WWTPs. Clinically relevant bacterial genera, Klebsiella and Enterococcus, found in both the BNR and AD sludges, were significantly correlated with the tetX gene. Throughout this study, the relationship between microbial communities and specific ARGs was revealed, illustrating that the composition of the microbial community could play a vital role in the abundance of ARGs. These results will better inform future studies aimed at controlling the spread of ARGs and their potential hosts from WWTPs.
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Affiliation(s)
- Shahbaz Raza
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Kyeong Hwan Kang
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Juhee Shin
- Department of Energy Engineering, Future Convergence Technology Research Institute, Gyeongsang National UniversityJinju, Gyeongnam, 52828, Republic of Korea
| | - Seung Gu Shin
- Department of Energy Engineering, Future Convergence Technology Research Institute, Gyeongsang National UniversityJinju, Gyeongnam, 52828, Republic of Korea; Department of Energy System Engineering, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Jihyun Chun
- Department of Marine Environmental Engineering, Gyeongsang National University, Tongyeong, Gyeongnam, 53064, Republic of Korea
| | - Hyun Uk Cho
- Department of Marine Environmental Engineering, Gyeongsang National University, Tongyeong, Gyeongnam, 53064, Republic of Korea
| | - Jingyeong Shin
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul, 04763, Republic of Korea; Bio Resource Center, Institute for Advanced Engineering, Yongin, Gyeonggi-do, 17180, Republic of Korea.
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul, 04763, Republic of Korea.
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Tiwari A, Kurittu P, Al-Mustapha AI, Heljanko V, Johansson V, Thakali O, Mishra SK, Lehto KM, Lipponen A, Oikarinen S, Pitkänen T, Heikinheimo A. Wastewater surveillance of antibiotic-resistant bacterial pathogens: A systematic review. Front Microbiol 2022; 13:977106. [PMID: 36590429 PMCID: PMC9798455 DOI: 10.3389/fmicb.2022.977106] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Infectious diseases caused by antibiotic-resistant bacterial (ARB) pathogens are a serious threat to human and animal health. The active surveillance of ARB using an integrated one-health approach can help to reduce the emergence and spread of ARB, reduce the associated economic impact, and guide antimicrobial stewardship programs. Wastewater surveillance (WWS) of ARB provides composite samples for a total population, with easy access to the mixed community microbiome. This concept is emerging rapidly, but the clinical utility, sensitivity, and uniformity of WWS of ARB remain poorly understood especially in relation to clinical evidence in sewershed communities. Here, we systematically searched the literature to identify studies that have compared findings from WWS of ARB and antibiotic resistance genes (ARG) with clinical evidence in parallel, thereby evaluating how likely WWS of ARB and ARG can relate to the clinical cases in communities. Initially, 2,235 articles were obtained using the primary search keywords, and 1,219 articles remained after de-duplication. Among these, 35 articles fulfilled the search criteria, and an additional 13 relevant articles were included by searching references in the primary literature. Among the 48 included papers, 34 studies used a culture-based method, followed by 11 metagenomics, and three PCR-based methods. A total of 28 out of 48 included studies were conducted at the single sewershed level, eight studies involved several countries, seven studies were conducted at national or regional scales, and five at hospital levels. Our review revealed that the performance of WWS of ARB pathogens has been evaluated more frequently for Escherichia coli, Enterococcus spp., and other members of the family Enterobacteriaceae, but has not been uniformly tested for all ARB pathogens. Many wastewater-based ARB studies comparing the findings with clinical evidence were conducted to evaluate the public health risk but not to relate with clinical evidence and to evaluate the performance of WWS of ARB. Indeed, relating WWS of ARB with clinical evidence in a sewershed is not straightforward, as the source of ARB in wastewater cannot be only from symptomatic human individuals but can also be from asymptomatic carriers as well as from animal sources. Further, the varying fates of each bacterial species and ARG within the sewerage make the aim of connecting WWS of ARB with clinical evidence more complicated. Therefore, future studies evaluating the performance of many AMR pathogens and their genes for WWS one by one can make the process simpler and the interpretation of results easier.
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Affiliation(s)
- Ananda Tiwari
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland,*Correspondence: Ananda Tiwari,
| | - Paula Kurittu
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ahmad I. Al-Mustapha
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland,Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria,Department of Veterinary Services, Kwara State Ministry of Agriculture and Rural Development, Ilorin, Nigeria
| | - Viivi Heljanko
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Venla Johansson
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ocean Thakali
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Shyam Kumar Mishra
- School of Optometry and Vision Science, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Kirsi-Maarit Lehto
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anssi Lipponen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Tarja Pitkänen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland,Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland,Finnish Food Authority, Seinäjoki, Finland
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30
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Kruglova A, Muñoz-Palazón B, Gonzalez-Martinez A, Mikola A, Vahala R, Talvitie J. The dangerous transporters: A study of microplastic-associated bacteria passing through municipal wastewater treatment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120316. [PMID: 36191797 DOI: 10.1016/j.envpol.2022.120316] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/12/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Microplastics (MPs) provide a stable and protective habitat for diverse wastewater bacteria, including pathogenic and antibiotic-resistant species. Therefore, MPs may potentially transport these bacteria through wastewater treatment steps to the environment and far distances. This study investigated bacterial communities of MP-associated bacteria from different stages of municipal wastewater treatment processes to evaluate the potential negative effect of these biofilms on the environment. The results showed a high diversity of bacteria that were strongly attached to MPs. After all treatment steps, the core bacterial groups remained attached to MPs and escaped from the wastewater treatment plant with effluent water. Several pathogenic bacteria were identified in MP samples from all treatment steps, and most of them were found in effluent water. These data provide new insights into the possible impacts of wastewater-derived MPs on the environment. MP-associated biofilms were proved to be important sources of pathogens and antibiotic-resistant genes in natural waters.
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Affiliation(s)
- Antonina Kruglova
- Department of Built Environment, Aalto University, PO Box 15200, FI-00076, AALTO, Finland.
| | - Barbara Muñoz-Palazón
- Department of Microbiology, University of Granada, Campus Universitario de la Cartuja C.P., 18071, Granada, Spain; Dipartimento di Ecologia e Biologia, Università degli Studi della Tuscia, Largo Università snc, 01100, Viterbo, Italy
| | - Alejandro Gonzalez-Martinez
- Department of Microbiology, University of Granada, Campus Universitario de la Cartuja C.P., 18071, Granada, Spain
| | - Anna Mikola
- Department of Built Environment, Aalto University, PO Box 15200, FI-00076, AALTO, Finland
| | - Riku Vahala
- Department of Built Environment, Aalto University, PO Box 15200, FI-00076, AALTO, Finland
| | - Julia Talvitie
- Marine Research Center, Finnish Environment Institute (SYKE), P.O.Box 140, FI-00251, Helsinki, Finland
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31
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Entezari S, Al MA, Mostashari A, Ganjidoust H, Ayati B, Yang J. Microplastics in urban waters and its effects on microbial communities: a critical review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:88410-88431. [PMID: 36327084 DOI: 10.1007/s11356-022-23810-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Microplastic (MP) pollution is one of the emerging threats to the water and terrestrial environment, forcing a new environmental challenge due to the growing trend of plastic released into the environment. Synthetic and non-synthetic plastic components can be found in rivers, lakes/reservoirs, oceans, mountains, and even remote areas, such as the Arctic and Antarctic ice sheets. MPs' main challenge is identifying, measuring, and evaluating their impacts on environmental behaviors, such as carbon and nutrient cycles, water and wastewater microbiome, and the associated side effects. However, until now, no standardized methodical protocols have been proposed for comparing the results of studies in different environments, especially in urban water and wastewater. This review briefly discusses MPs' sources, fate, and transport in urban waters and explains methodological uncertainty. The effects of MPs on urban water microbiomes, including urban runoff, sewage wastewater, stagnant water in plumbing networks, etc., are also examined in depth. Furthermore, this study highlights the pathway of MPs and their transport vectors to different parts of ecosystems and human life, particularly through mediating microbial communities, antibiotic-resistant genes, and biogeochemical cycles. Overall, we have briefly highlighted the present research gaps, the lack of appropriate policy for evaluating microplastics and their interactions with urban water microbiomes, and possible future initiatives.
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Affiliation(s)
- Saber Entezari
- Environmental Engineering Division, Faculty of Civil & Env. Eng., TMU, Tehran, Iran
| | - Mamun Abdullah Al
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, 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, Beijing, 100049, China
| | - Amir Mostashari
- Environmental Engineering Division, Faculty of Civil & Env. Eng., TMU, Tehran, Iran
| | - Hossein Ganjidoust
- Environmental Engineering Division, Faculty of Civil & Env. Eng., TMU, Tehran, Iran.
| | - Bita Ayati
- Environmental Engineering Division, Faculty of Civil & Env. Eng., TMU, Tehran, Iran
| | - Jun Yang
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
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32
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Chen T, Zhang S, Zhu R, Zhao M, Zhang Y, Wang Y, Liao X, Wu Y, Mi J. Distribution and driving factors of antibiotic resistance genes in treated wastewater from different types of livestock farms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157837. [PMID: 35934031 DOI: 10.1016/j.scitotenv.2022.157837] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Treated wastewater from livestock farms is an important reservoir for antibiotic resistance genes (ARGs), and is a main source of ARGs in the environment. However, the distribution and driving factors of ARGs in treated wastewater from different types of livestock farms are rarely reported. In this study, treated wastewater from 69 large-scale livestock farms of different types, including broiler, layer, and pig farms, was collected, and 11 subtypes of ARGs, 2 mobile genetic elements (MGEs) and bacterial community structure were analyzed. The results revealed detection rates of NDM-1 and mcr-1 of 90 % and 43 %, respectively, and the detection rates of other ARGs were 100 %. The relative abundance of ARGs, such as tetA, tetX and strB, in broiler farms was significantly higher than that in layer farms, but the bacterial α diversity was significantly lower than that in other farm types. Furthermore, although the treatment process had a greater impact on the physicochemical properties of the treated wastewater than the livestock type, livestock type was the main factor affecting the bacterial community in the treated wastewater. The analysis of potential host bacteria of ARGs revealed significant differences in the host bacteria of ARGs in treated wastewater from different types of livestock farms. The host bacteria of ARGs in broiler farms mainly belonged to Actinobacteria, layer farms mainly belonged to Proteobacteria, and pig farms mainly belonged to Firmicutes. Additionally, redundancy analysis showed that the distribution of ARGs may have resulted from the combination of multiple driving factors in different types of livestock farms, among which tnpA and NH4+-N were the main influencing factors. This study revealed multiple driving factors for the distribution of typical ARGs in treated wastewater from different types of livestock farms, providing basic data for the prevention and control of ARG pollution in agricultural environments.
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Affiliation(s)
- Tao Chen
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Shiyu Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Run Zhu
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Minxing Zhao
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yu Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yan Wang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Xindi Liao
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Yinbao Wu
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China.
| | - Jiandui Mi
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China.
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33
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Sun G, Zhang Q, Dong Z, Dong D, Fang H, Wang C, Dong Y, Wu J, Tan X, Zhu P, Wan Y. Antibiotic resistant bacteria: A bibliometric review of literature. Front Public Health 2022; 10:1002015. [PMID: 36466520 PMCID: PMC9713414 DOI: 10.3389/fpubh.2022.1002015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022] Open
Abstract
Antibiotic-resistant bacteria (ARB) are a serious threat to the health of people and the ecological environment. With this problem becoming more and more serious, more countries made research on the ARB, and the research number has been sharply increased particularly over the past decade. Therefore, it is quite necessary to globally retrace relevant researches on the ARB published from 2010 to 2020. This will help researchers to understand the current research situation, research trends and research hotspots in this field. This paper uses bibliometrics to examine publications in the field of ARB from 2010 to 2020 that were retrieved from the Web of Science (WOS). Our study performed a statistical analysis of the countries, institutions, journals, authors, research areas, author keywords, Essential Science Indicators (ESI) highly cited papers, and ESI hotspots papers to provide an overview of the ARB field as well as research trends, research hotspots, and future research directions in the field. The results showed that the number of related studies is increasing year by year; the USA is most published in the field of ARB; China is the most active in this field in the recent years; the Chinese Acad Sci published the most articles; Sci. Total Environ. published the greatest number of articles; CM Manaia has the most contributions; Environmental Sciences and Ecology is the most popular research area; and "antibiotic resistance," "antibiotics," and "antibiotic resistance genes" were the most frequently occurring author keywords. A citation analysis showed that aquatic environment-related antibiotic resistance is a key research area in this field, while antimicrobial nanomaterial-related research is a recent popular topic.
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Affiliation(s)
- Guojun Sun
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Qian Zhang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Zuojun Dong
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Dashun Dong
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Hui Fang
- Institute of Information Resource, Zhejiang University of Technology, Hangzhou, China
| | - Chaojun Wang
- Hangzhou Aeronautical Sanatorium for Special Service of Chinese Air Force, Hangzhou, China
| | - Yichen Dong
- Department of Chinese Medicine, Macau University of Science and Technology, Taipa, Macau SAR, China
| | - Jiezhou Wu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Xuanzhe Tan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Peiyao Zhu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Yuehua Wan
- Institute of Information Resource, Zhejiang University of Technology, Hangzhou, China
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34
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Chen T, Zhao M, Tang X, Wang W, Zhang M, Tang J, Wang W, Wei W, Ma B, Zou Y, Zhang N, Mi J, Wang Y, Liao X, Wu Y. Serious Risk of Tigecycline Resistance in Escherichia coli Isolated from Swine Manure. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02133-2. [PMID: 36326874 DOI: 10.1007/s00248-022-02133-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The emergence of the plasmid-mediated tigecycline resistance gene tetX family in pig farms has attracted worldwide attention. The use of tetracycline antibiotics in pig farms has a facilitating effect on the prevalence of the tetX family, but the relationship among its presence, expression, and resistance phenotype in resistant bacteria is unknown. In this study, the presence and expression characteristics of tetracycline resistance genes (TRGs) in 89 strains of doxycycline-resistant E. coli (DRE) isolated from pig manure samples from 20 pig farms under low concentrations of doxycycline stress (2 μg/mL) were analyzed. The detection rate of tetO was 96.63%, which is higher than those of other TRGs, such as tetA (94.38%), tetX (76.40%), tetB (73.03%), and tet(X4) (69.66%). At least three TRG types were present in DRE strains, which thus showed extensive resistance to tetracycline antibiotics, and 37% of these strains were resistant to tigecycline. In the presence of a low concentration of doxycycline, tetA played an important role, and the expression and existence ratio of TRGs indicated low expression of TRGs. Furthermore, the doxycycline resistance of DRE was jointly determined by the total absolute abundance of TRGs, and the absolute abundance of tetX and tet(X4) was significantly positively associated with tigecycline resistance in DRE (P < 0.05). Overall, DRE isolated from swine manure is an important reservoir of the tetX family, which suggests that DRE in swine manure has a high risk of tigecycline resistance, poses a potential threat to human health, and should be of public concern.
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Affiliation(s)
- Tao Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Minxing Zhao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoyue Tang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Wenqiang Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Miao Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Jing Tang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Wenxiao Wei
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Baohua Ma
- Foshan Customs Comprehensive Technology Center, 528200, Foshan, China
| | - Yongde Zou
- Foshan Customs Comprehensive Technology Center, 528200, Foshan, China
| | - Na Zhang
- Foshan Customs Comprehensive Technology Center, 528200, Foshan, China
| | - Jiandui Mi
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong, 525000, China
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing, China
- Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong, 525000, China
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing, China
- Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong, 525000, China
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing, China
- Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong, 525000, China.
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing, China.
- Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou, 510642, China.
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35
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Kneis D, Berendonk TU, Forslund SK, Hess S. Antibiotic Resistance Genes in River Biofilms: A Metagenomic Approach toward the Identification of Sources and Candidate Hosts. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14913-14922. [PMID: 35468283 PMCID: PMC9631990 DOI: 10.1021/acs.est.2c00370] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Treated wastewater is a major pathway by which antibiotic resistance genes (ARG) enter aquatic ecosystems. However, knowledge gaps remain concerning the dissemination of specific ARG and their association with bacterial hosts. Here, we employed shotgun metagenomics to track ARG and taxonomic markers in river biofilms along a gradient of fecal pollution depicted by crAssphage signatures. We found strong evidence for an impact of wastewater effluents on both community composition and resistomes. In the light of such simultaneity, we employed a model comparison technique to identify ARG-host relationships from nonassembled metagenomic DNA. Hereby, a major cause of spurious associations otherwise encountered in correlation-based ARG-host analyses was suppressed. For several families of ARG, namely those conferring resistance to beta-lactams, particular bacterial orders were identified as candidate hosts. The found associations of blaFOX and cphA with Aeromonadales or blaPER with Chromatiales support the outcome of independent evolutionary analyses and thus confirm the potential of the methodology. For other ARG families including blaIMP or tet, clusters of bacterial orders were identified which potentially harbor a major proportion of host species. For yet other ARG, like, for example, ant or erm, no particular host candidates were identifiable, indicating their spread across various taxonomic groups.
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Affiliation(s)
- David Kneis
- Technische
Universität Dresden, Institute of
Hydrobiology, 01062 Dresden, Germany
| | - Thomas U. Berendonk
- Technische
Universität Dresden, Institute of
Hydrobiology, 01062 Dresden, Germany
| | - Sofia K. Forslund
- Experimental
and Clinical Research Center, Charitéplatz 1, 10117 Berlin, Germany
- Max
Delbrück Center for Molecular Medicine, R.-Rössle-Straße 10, 13125 Berlin, Germany
- Charité
University Hospital, Charitéplatz 1, 10117 Berlin, Germany
- German
Centre for Cardiovascular Research, Potsdamer Straße 58, 10785 Berlin, Germany
- European
Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Stefanie Hess
- TU
Dresden, Institute of Microbiology, 01062 Dresden, Germany
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36
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Knecht CA, Krüger M, Kellmann S, Mäusezahl I, Möder M, Adelowo OO, Vollmers J, Kaster AK, Nivala J, Müller JA. Cellular stress affects the fate of microbial resistance to folate inhibitors in treatment wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157318. [PMID: 35839882 DOI: 10.1016/j.scitotenv.2022.157318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/11/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
The environmental prevalence of antimicrobial resistance (AMR) has come into focus under the One Health concept. Wastewater treatment systems are among the significant sources of AMR in the environment. In such systems, it is uncertain to which extent antimicrobials present at sub-inhibitory concentrations constitute a selective pressure for bacterial maintenance and acquisition of antibiotic resistance (AR) genes. Here, we mapped AMR to inhibitors of folate biosynthesis in an aerated and a non-aerated horizontal subsurface flow treatment wetland receiving the same pre-treated municipal wastewater. General water characteristics and the concentrations of folate inhibitors were determined to define the ambient conditions over the longitudinal axis of the two treatment wetlands. Profiling of AMR as well as class 1 integrons, a carrier of AR genes against folate inhibitors and other antimicrobials, was conducted by cultivation-dependent and -independent methods. The wetlands achieved mean reductions of AR gene copy numbers in the effluents of at least 2 log, with the aerated system performing better. The folate inhibitors had no noticeable effect on the prevalence of respective AR genes. However, there was a transient increase of AR gene copy numbers and AR gene cassette composition in class 1 integrons in the aerated wetland. The comparison of all data from both wetlands suggests that higher levels of cellular stress in the aerated system promoted the mobility of AR genes via enhancing the activity of the DNA recombinase of the class 1 integron. The findings highlight that environmental conditions that modulate the activity of this genetic element can be more important for the fate of associated AR genes in treatment wetlands than the ambient concentration of the respective antimicrobial agents. By extrapolation, the results suggest that cellular stress also contributes to the mobility of AR gene in other wastewater treatment systems.
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Affiliation(s)
- Camila A Knecht
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Otto-von-Guericke-University Magdeburg, FVST Chair Environmental Technology, Magdeburg, Germany
| | - Markus Krüger
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Institute of Biodiversity, Friedrich-Schiller-University Jena, Germany
| | - Simon Kellmann
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ines Mäusezahl
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Monika Möder
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Olawale O Adelowo
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria
| | - John Vollmers
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Jaime Nivala
- Environmental and Biotechnology Centre (UBZ), Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany; Research Unit REVERSAAL, National Research Institute for Agriculture, Food and the Environment (INRAE), Villeurbanne, France
| | - Jochen A Müller
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.
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Muurinen J, Muziasari WI, Hultman J, Pärnänen K, Narita V, Lyra C, Fadlillah LN, Rizki LP, Nurmi W, Tiedje JM, Dwiprahasto I, Hadi P, Virta MPJ. Antibiotic Resistomes and Microbiomes in the Surface Water along the Code River in Indonesia Reflect Drainage Basin Anthropogenic Activities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14994-15006. [PMID: 35775832 PMCID: PMC9631996 DOI: 10.1021/acs.est.2c01570] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Water and sanitation are important factors in the emergence of antimicrobial resistance in low- and middle-income countries. Drug residues, metals, and various wastes foster the spread of antibiotic resistance genes (ARGs) with the help of mobile genetic elements (MGEs), and therefore, rivers receiving contaminants and effluents from multiple sources are of special interest. We followed both the microbiome and resistome of the Code River in Indonesia from its pristine origin at the Merapi volcano through rural and then city areas to the coast of the Indian Ocean. We used a SmartChip quantitative PCR with 382 primer pairs for profiling the resistome and MGEs and 16S rRNA gene amplicon sequencing to analyze the bacterial communities. The community structure explained the resistome composition in rural areas, while the city sampling sites had lower bacterial diversity and more ARGs, which correlated with MGEs, suggesting increased mobility potential in response to pressures from human activities. Importantly, the vast majority of ARGs and MGEs were no longer detectable in marine waters at the ocean entrance. Our work provides information on the impact of different influents on river health as well as sheds light on how land use contributes to the river resistome and microbiome.
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Affiliation(s)
- Johanna Muurinen
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Windi I. Muziasari
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
- Resistomap
Oy, Viikinkaari 4, 00790 Helsinki, Finland
| | - Jenni Hultman
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Katariina Pärnänen
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Vanny Narita
- PT.
AmonRa, Jalan Panti Asuhan
37, 13330 Jakarta
Timur, Indonesia
| | - Christina Lyra
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Lintang N. Fadlillah
- Center
for Environmental Studies (PSLH), Universitas
Gadjah Mada, Jalan Kuningan, 55281 Yogyakarta, Indonesia
- Faculty
of Geography, Universitas Gadjah Mada, Jalan Kaliurang, 55281 Yogyakarta, Indonesia
| | - Ludhang P. Rizki
- Center
for Environmental Studies (PSLH), Universitas
Gadjah Mada, Jalan Kuningan, 55281 Yogyakarta, Indonesia
- Faculty of
Medicine, Universitas Gadjah Mada, Jalan Farmako, 55281 Yogyakarta, Indonesia
| | - William Nurmi
- Resistomap
Oy, Viikinkaari 4, 00790 Helsinki, Finland
| | - James M. Tiedje
- Center
for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, United States
| | - Iwan Dwiprahasto
- Faculty of
Medicine, Universitas Gadjah Mada, Jalan Farmako, 55281 Yogyakarta, Indonesia
| | - Pramono Hadi
- Center
for Environmental Studies (PSLH), Universitas
Gadjah Mada, Jalan Kuningan, 55281 Yogyakarta, Indonesia
- Faculty
of Geography, Universitas Gadjah Mada, Jalan Kaliurang, 55281 Yogyakarta, Indonesia
| | - Marko P. J. Virta
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
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Wu Z, Che Y, Dang C, Zhang M, Zhang X, Sun Y, Li X, Zhang T, Xia Y. Nanopore-based long-read metagenomics uncover the resistome intrusion by antibiotic resistant bacteria from treated wastewater in receiving water body. WATER RESEARCH 2022; 226:119282. [PMID: 36332295 DOI: 10.1016/j.watres.2022.119282] [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: 07/13/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Wastewater treatment plant (WWTP) effluent discharge could induce the resistome enrichment in the receiving water environments. However, because of the general lack of a robust antibiotic-resistant bacteria (ARB) identification method, the driving mechanism for resistome accumulation in receiving environment is unclear. Here, we took advantage of the enhanced ARBs recognition by nanopore long reads to distinguish the indigenous ARBs and the accumulation of WWTP-borne ARBs in the receiving water body of a domestic WWTP. A bioinformatic framework (named ARGpore2: https://github.com/sustc-xylab/ARGpore2) was constructed and evaluate to facilitate antibiotic resistance genes (ARGs) and ARBs identification in nanopore reads. ARGs identification by ARGpore2 showed comparable precision and recall to that of the commonly adopt BLASTP-based method, whereas the spectrum of ARBs doubled that of the assembled Illumina dataset. Totally, we identified 33 ARBs genera carrying 65 ARG subtypes in the receiving seawater, whose concentration was in general 10 times higher than clean seawater's. Notably we report a primary resistome intrusion caused by the revival of residual microbes survived from disinfection treatment. These WWTP-borne ARBs, including several animal/human enteric pathogens, contributed up to 85% of the receiving water resistome. Plasmids and class 1 integrons were reckoned as major vehicles facilitating the persistence and dissemination of ARGs. Moreover, our work demonstrated the importance of extensive carrier identification in determining the driving force of multifactor coupled resistome booming in complicated environmental conditions, thereby paving the way for establishing priority for effective ARGs mitigation strategies.
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Affiliation(s)
- Ziqi Wu
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - You Che
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR
| | - Chenyuan Dang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Miao Zhang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuyang Zhang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuhong Sun
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiang Li
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR
| | - Yu Xia
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
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Spatiotemporal Investigation of Antibiotic Resistance in the Urban Water Cycle Influenced by Environmental and Anthropogenic Activity. Microbiol Spectr 2022; 10:e0247322. [PMID: 36036576 PMCID: PMC9603458 DOI: 10.1128/spectrum.02473-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
With increasing emergence of antimicrobial resistant bacteria (ARB) and the risk this poses to public health, there are growing concerns regarding water pollution contributing to the spread of antimicrobial resistance (AMR) through inadequate amenities and the rapid rate of urbanization. In this study, the impact of different anthropogenic factors on the prevalence of AMR in the urban water cycle in Stellenbosch, South Africa (SA) was examined. Carbapenem, colistin, gentamicin and sulfamethoxazole resistant Gram-negative bacteria were recovered by selectively culturing aqueous, biofilm and sediment samples from sites impacted to varying degrees by informal settlements, residential, industrial, and agricultural activities, as well as a municipal wastewater treatment works (WWTW). A metagenomic approach determined community profiles and dominant AMR genes at various sites, while carbapenem resistant colonies were characterized using whole genome sequencing (WGS). Isolates recovered from agricultural sites exhibited relatively high levels of resistance to carbapenems and colistin, whereas sites impacted by domestic run-off had a higher prevalence of resistance to gentamicin and sulfamethoxazole, corresponding to usage data in SA. Similar microbial taxa were identified in raw sewage, sites downstream of informal settlements, and industrial areas that have limited waste removal infrastructure while WWTW were seen to reduce the prevalence of ARB in treated wastewater when operating efficiently. The results indicate the multiple complex drivers underpinning environmental dissemination of AMR and suggest that WWTW assist in removing AMR from the environment, reinforcing the necessity of adequate waste removal infrastructure and antibiotic stewardship measures to mitigate AMR transmission. IMPORTANCE The results from this study are of importance as they fill a gap in the data available on environmental AMR in South Africa to date. This study was done in parallel with co-investigators focusing on the prevalence of various antimicrobials at the same sites selected in our study, verifying that the sites that are influenced by informal settlements and WWTW influent had higher concentrations of antimicrobials and antimicrobial metabolites. The various locations of the sample sites selected, the frequency of the samples collected over a year, and the different types of samples collected at each site all contribute to informing how AMR in the environment might be affected by anthropogenic activity.
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Leal dos Santos D, Chaúque BJM, Virginio VG, Cossa VC, Pettan-Brewer C, Schrekker HS, Rott MB. Occurrence of Naegleria fowleri and their implication for health - a look under the One Health approaches. Int J Hyg Environ Health 2022; 246:114053. [DOI: 10.1016/j.ijheh.2022.114053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022]
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Sekizuka T, Itokawa K, Tanaka R, Hashino M, Yatsu K, Kuroda M. Metagenomic Analysis of Urban Wastewater Treatment Plant Effluents in Tokyo. Infect Drug Resist 2022; 15:4763-4777. [PMID: 36039320 PMCID: PMC9419991 DOI: 10.2147/idr.s370669] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Urban wastewater treatment plant (WWTP) effluents, even with proper treatment, may cause antimicrobial resistance (AMR) burden, with a high frequency of acquired antimicrobial resistance genes (ARGs). The dissemination of ARGs into the environment increases the risk of infectious diseases; however, there is little direct evidence regarding their epidemiological effects. This study aimed to assess effluents from urban WWTPs around the Tama River and Tokyo Bay using metagenomic analysis of (AMR) genes (ARGs) and heavy-metal resistance genes. Methods Metagenomic DNA-seq analysis of water samples and resistome analysis were performed. Results The most prevalent ARG was the sulfonamide resistance gene, sul1, followed by the quaternary ammonium compound resistance gene, qacE, suggesting that basic gene sets (sul1 and ∆qacE) in the class 1 integrons are the predominant ARGs. The aminoglycoside resistance genes, aadA and aph, and macrolide resistance genes, msr(E) and mph(E), were the predominant ARGs against each antimicrobial. bla OXA and bla GES were frequently detected, whereas the bla CTX-M cluster was faintly detected. Non-metric multidimensional scaling plot analysis and canonical correspondence analysis results suggested that marked differences in ARGs could be involved in the seasonal differences; qnrS2, aac(6')-Ib, and mef(C) increased markedly in summer, whereas msr(E) was more frequently detected in winter. Heavy-metal (Hg and Cu) resistance genes (HMRGs) were significantly detected in effluents from all WWTPs. Conclusion We characterized a baseline level of the environmental ARG/HMRG profile in the overall community, suggesting that environmental AMR surveillance, particularly in urban WWTPs, is a valuable first step in monitoring the AMR dissemination of bacteria from predominantly healthy individuals carrying notable ARG/Bs.
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Affiliation(s)
- Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Kentaro Itokawa
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Rina Tanaka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Masanori Hashino
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Koji Yatsu
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
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Philips JG, Martin-Avila E, Robold AV. Horizontal gene transfer from genetically modified plants - Regulatory considerations. Front Bioeng Biotechnol 2022; 10:971402. [PMID: 36118580 PMCID: PMC9471246 DOI: 10.3389/fbioe.2022.971402] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Gene technology regulators receive applications seeking permission for the environmental release of genetically modified (GM) plants, many of which possess beneficial traits such as improved production, enhanced nutrition and resistance to drought, pests and diseases. The regulators must assess the risks to human and animal health and to the environment from releasing these GM plants. One such consideration, of many, is the likelihood and potential consequence of the introduced or modified DNA being transferred to other organisms, including people. While such gene transfer is most likely to occur to sexually compatible relatives (vertical gene transfer), horizontal gene transfer (HGT), which is the acquisition of genetic material that has not been inherited from a parent, is also a possibility considered during these assessments. Advances in HGT detection, aided by next generation sequencing, have demonstrated that HGT occurrence may have been previously underestimated. In this review, we provide updated evidence on the likelihood, factors and the barriers for the introduced or modified DNA in GM plants to be horizontally transferred into a variety of recipients. We present the legislation and frameworks the Australian Gene Technology Regulator adheres to with respect to the consideration of risks posed by HGT. Such a perspective may generally be applicable to regulators in other jurisdictions as well as to commercial and research organisations who develop GM plants.
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Roguet A, Newton RJ, Eren AM, McLellan SL. Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure. mSystems 2022; 7:e0011822. [PMID: 35762794 PMCID: PMC9426572 DOI: 10.1128/msystems.00118-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/25/2022] [Indexed: 11/20/2022] Open
Abstract
Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates back only ~150 years. Sewer pipes transport human waste and provide a view into public health, but the resident organisms that likely modulate these features are relatively unexplored. Here, we show that the bacterial assemblages sequenced from untreated wastewater in 71 U.S. cities were highly coherent at a fine sequence level, suggesting that urban infrastructure separated by great spatial distances can give rise to strikingly similar communities. Within the overall microbial community structure, temperature had a discernible impact on the distribution patterns of closely related amplicon sequence variants, resulting in warm and cold ecotypes. Two bacterial genera were dominant in most cities regardless of their size or geographic location; on average, Arcobacter accounted for 11% and Acinetobacter 10% of the entire community. Metagenomic analysis of six cities revealed these highly abundant resident organisms carry clinically important antibiotic resistant genes blaCTX-M, blaOXA, and blaTEM. In contrast, human fecal bacteria account for only ~13% of the community; therefore, antibiotic resistance gene inputs from human sources to the sewer system could be comparatively small, which will impact measurement capabilities when monitoring human populations using wastewater. With growing awareness of the metabolic potential of microbes within these vast networks of pipes and the ability to examine the health of human populations, it is timely to increase our understanding of the ecology of these systems. IMPORTANCE Sewer infrastructure is a relatively new habitat comprised of thousands of kilometers of pipes beneath cities. These wastewater conveyance systems contain large reservoirs of microbial biomass with a wide range of metabolic potential and are significant reservoirs of antibiotic resistant organisms; however, we lack an adequate understanding of the ecology or activity of these communities beyond wastewater treatment plants. The striking coherence of the sewer microbiome across the United States demonstrates that the sewer environment is highly selective for a particular microbial community composition. Therefore, results from more in-depth studies or proven engineering controls in one system could be extrapolated more broadly. Understanding the complex ecology of sewer infrastructure is critical for not only improving our ability to treat human waste and increasing the sustainability of our cities but also to create scalable and effective sewage microbial observatories, which are inevitable investments of the future to monitor health in human populations.
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Affiliation(s)
- Adélaïde Roguet
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Ryan J. Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - A. Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Sandra L. McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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Ke M, Feng L, Huang S, Lu T, Yu Z, Yang Y, Hu H, Peijnenburg WJGM, Feng L, Qian H. Development of a Potentially New Algaecide for Controlling Harmful Cyanobacteria Blooms Which is Ecologically Safe and Selective. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10134-10143. [PMID: 35972278 DOI: 10.1021/acs.jafc.2c02489] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Harmful cyanobacterial blooms (HCBs) caused by Microcystis aeruginosa are of great concern as they negatively affect the aquatic environment and human health. Chemical methods could rapidly eradicate HCBs and have been used for many decades. However, many chemical reagents are not recommended to eliminate HCBs in the long term, given the possible destructive and toxic effects of the chemicals employed on non-target aquatic organisms. We developed a new algaecide, 2-((1,3,4-thiadiazol-2-yl)thio)-N-(4-chlorophenyl) acetamide (Q2), to control harmful cyanobacteria while being environmentally friendly and selective. In our study, Q2 effectively inhibited cyanobacterial growth, especially of M. aeruginosa, but did not affect eukaryotic algae in test concentrations. A critical mechanism was revealed by transcriptome and metagenomic results showing that Q2 affects multiple cellular targets of cyanobacteria for HCB control, including the destruction of organelles, damage in the photosynthesis center, as well as inhibition of gas vesicle growth, and these changes can be highly relevant to the decrease of quorum-sensing functional KEGG pathways. Furthermore, Q2 did not affect the microbial composition and could recover the disrupted aquatic functional pathways in a short period. This is different from the impact on ecosystem functioning of the traditionally used harmful algaecide diuron. All these results verified that Q2 could be friendly to the aquatic environment, providing a new directional choice in managing HCBs in the future.
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Affiliation(s)
- Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou310014, China
| | - Lan Feng
- College of Environment, Zhejiang University of Technology, Hangzhou310014, China
| | - Shi Huang
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education; College of Chemistry, Central China Normal University, Wuhan430079, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou310014, China
| | - Zhitao Yu
- College of Environment, Zhejiang University of Technology, Hangzhou310014, China
| | - Yaohui Yang
- College of Environment, Zhejiang University of Technology, Hangzhou310014, China
| | - Hang Hu
- College of Environment, Zhejiang University of Technology, Hangzhou310014, China
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, Leiden2300 RA, The Netherlands
- Center for Safety of Substances and Products, National Institute of Public Health and the Environment (RIVM), P.O. Box 1, Bilthoven3720, The Netherlands
| | - Lingling Feng
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education; College of Chemistry, Central China Normal University, Wuhan430079, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou310014, China
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Das S, Bombaywala S, Srivastava S, Kapley A, Dhodapkar R, Dafale NA. Genome plasticity as a paradigm of antibiotic resistance spread in ESKAPE pathogens. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:40507-40519. [PMID: 35349073 DOI: 10.1007/s11356-022-19840-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The major reason behind the spread of antibiotic resistance genes (ARGs) is persistent selective pressure in the environment encountered by bacteria. Genome plasticity plays a crucial role in dissemination of antibiotic resistance among bacterial pathogens. Mobile genetic elements harboring ARGs are reported to dodge bacterial immune system and mediate horizontal gene transfer (HGT) under selective pressure. Residual antibiotic pollutants develop selective pressures that force the bacteria to lose their defense mechanisms (CRISPR-cas) and acquire resistance. The present study targets the ESKAPE organisms (namely, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) causing various nosocomial infections and emerging multidrug-resistant species. The role of CRISPR-cas systems in inhibition of HGT in prokaryotes and its loss due to presence of various stressors in the environment is also focused in the study. IncF and IncH plasmids were identified in all strains of E. faecalis and K. pneumoniae, carrying Beta-lactam and fluoroquinolone resistance genes, whereas sal3, phiCTX, and SEN34 prophages harbored aminoglycoside resistance genes (aadA, aac). Various MGEs present in selected environmental niches that aid the bacterial genome plasticity and transfer of ARGs contributing to its spread are also identified.
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Affiliation(s)
- Sanchita Das
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
| | - Sakina Bombaywala
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 2010 20, India
| | - Shweta Srivastava
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 2010 20, India
| | - Atya Kapley
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
| | - Rita Dhodapkar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
| | - Nishant A Dafale
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 2010 20, India.
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Yang T, Jiang L, Bi X, Cheng L, Zheng X, Wang X, Zhou X. Submicron aerosols share potential pathogens and antibiotic resistomes with wastewater or sludge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153521. [PMID: 35104511 DOI: 10.1016/j.scitotenv.2022.153521] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Generation of size-segregated aerosols is an important eco-environmental problem in wastewater treatment plants (WWTPs), but the characteristics of potential pathogens and antibiotic resistomes in submicron aerosols (PM1.0) were almost unknown. Here, 16S rRNA gene amplification and shotgun metagenome sequencing were respectively used to study the profiles of potential pathogens and antibiotic resistance genes (ARGs) in PM1.0 from a full-scale WWTP. Acinetobacter and sul1 were respectively the predominant potential pathogens and ARG subtypes in PM1.0 from aeration process. A total of 9 potential pathogens and 147 ARG subtypes, were shared among WWTP-PM1.0, wastewater/sludge, and ambient air. Significant differences of potential pathogens or ARGs were found between WWTP-PM1.0 and wastewater/sludge, however, wastewater/sludge had more crucial source contribution than the ambient air. Moreover, 13 potential pathogens and 40 ARG subtypes were easily aerosolized in PM1.0 from at least one of the treatment units. ARGs were mainly harbored by Proteobacteria, and multidrug resistance genes were the most ARG type carried by potential pathogens. Taken together, this study indicates the prevalence of potential pathogens, ARGs, and ARG-carrying potential pathogens in WWTP-PM1.0, which highlights the potential risk of PM1.0 in spreading potential pathogens and antibiotic resistomes into the air environments.
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Affiliation(s)
- Tang Yang
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266033, PR China
| | - Lu Jiang
- College of Oceanic and Atmospheric Sciences, Ocean University of China, Qingdao 266100, PR China.
| | - Xuejun Bi
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266033, PR China
| | - Lihua Cheng
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266033, PR China.
| | - Xiang Zheng
- School of Environment & Natural Resources, Renmin University of China, Beijing 100872, PR China
| | - Xiaodong Wang
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266033, PR China
| | - Xiaolin Zhou
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266033, PR China
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Wei Z, Shen W, Feng K, Feng Y, He Z, Li Y, Jiang C, Liu S, Zhu YG, Deng Y. Organic fertilizer potentiates the transfer of typical antibiotic resistance gene among special bacterial species. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:128985. [PMID: 35483268 DOI: 10.1016/j.jhazmat.2022.128985] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 02/05/2023]
Abstract
The propagation of antibiotic resistance genes (ARGs) in environments has evoked many attentions, however, how to identify their host pathogenic bacteria in situ remains a great challenge. Here we explored the bacterial host distribution and dissemination of a typical ARG, sul1 gene, in agricultural soils through the simultaneous detection of sul1 and its host 16S rRNA gene by emulsion paired isolation and concatenation PCR (epicPCR). Compared to chemical fertilizer, organic fertilizer (chicken manure) led to a higher prevalence of sul1 gene in the soil, and dominant bacterial hosts of sul1 gene were classified into Proteobacteria and Bacteroidetes phyla. Additionally, significant higher diversity of antibiotic resistance bacteria (ARB), higher rate of horizontal gene transfer (HGT), higher rate of mobile genetic elements (MGE) and higher proportion of pathogens were all observed in the treatment of organic fertilizer. This study alerts potential health risks of manure applications in agricultural soils.
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Affiliation(s)
- Ziyan Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Wenli Shen
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Youzhi Feng
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Yan Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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Yuan T, Lin ZB, Cheng S, Wang R, Lu P. Removal of Sulfonamide Resistance Genes in Fishery Reclamation Mining Subsidence Area by Zeolite. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074281. [PMID: 35409961 PMCID: PMC8998867 DOI: 10.3390/ijerph19074281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 12/03/2022]
Abstract
A majority of subsidence lakes were reclaimed as fish ponds, but the widespread use of antibiotics has caused the pollution of antibiotic resistance genes (ARGs). This paper uses zeolite as a filter material to construct a horizontal submersible wastewater treatment device and explores its effect on the removal of conventional pollutants and sulfonamide ARGs in wastewater. The results showed that the removal of total nitrogen and ammonia nitrogen by the zeolite filter media were 59.0% and 63.8%, respectively, which were higher than the removal of total phosphorus and COD. The absolute abundances of sul1 and sul2 in wastewater were 2.81 × 104 copies·L−1 and 2.42 × 103 copies·L−1. On average, 60.62% of sul1 and 75.84% of sul2 can be removed, and more than 90% of sul1 and sul2 can be removed. Experiments showed that the residence time of wastewater in the treatment device had a significant impact on removal. The microbial community structure of aquaculture wastewater was quite different before and after wastewater treatment. The abundance changes of Saccharimonadales and Mycobacterium affect the removal of sulfonamide ARGs.
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Affiliation(s)
- Tao Yuan
- School of Architectural Decoration, Jiangsu Vocational Institute of Architectural Technology, Xuzhou 221000, China;
| | - Zi-Bo Lin
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221000, China; (Z.-B.L.); (S.C.); (R.W.)
| | - Sen Cheng
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221000, China; (Z.-B.L.); (S.C.); (R.W.)
| | - Rui Wang
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221000, China; (Z.-B.L.); (S.C.); (R.W.)
| | - Ping Lu
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221000, China; (Z.-B.L.); (S.C.); (R.W.)
- Correspondence:
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Zhang R, Yang S, An Y, Wang Y, Lei Y, Song L. Antibiotics and antibiotic resistance genes in landfills: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150647. [PMID: 34597560 DOI: 10.1016/j.scitotenv.2021.150647] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Landfill are important reservoirs of antibiotics and antibiotic resistance genes (ARGs). They harbor diverse contaminants, such as heavy metals and persistent organic chemicals, complex microbial consortia, and anaerobic degradation processes, which facilitate the occurrence, development, and transfer of ARGs and antibiotic resistant bacteria (ARB). The main concern is that antibiotics and developed ARGs and ARB may transfer to the local environment via leachate and landfill leakage. In this paper, we provide an overview of established studies on antibiotics and ARGs in landfills, summarize the origins and distribution of antibiotics and ARGs, discuss the linkages among various antibiotics, ARGs, and bacterial communities as well as the influencing factors of ARGs, and evaluate the current treatment processes of antibiotics and ARGs. Finally, future research is proposed to fill the current knowledge gaps, which include mechanisms for the development and transmission of antibiotic resistance, as well as efficient treatment approaches for antibiotic resistance.
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Affiliation(s)
- Rui Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 101407, China
| | - Shu Yang
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Yuwei An
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing 400714, China
| | - Yangqing Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing 400714, China
| | - Yu Lei
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing 400714, China
| | - Liyan Song
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing 400714, China; School of resources and environmental engineering, Anhui University, Hefei 230601, China.
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Dai D, Brown C, Bürgmann H, Larsson DGJ, Nambi I, Zhang T, Flach CF, Pruden A, Vikesland PJ. Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge. MICROBIOME 2022; 10:20. [PMID: 35093160 PMCID: PMC8801152 DOI: 10.1186/s40168-021-01216-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND There is concern that the microbially rich activated sludge environment of wastewater treatment plants (WWTPs) may contribute to the dissemination of antibiotic resistance genes (ARGs). We applied long-read (nanopore) sequencing to profile ARGs and their neighboring genes to illuminate their fate in the activated sludge treatment by comparing their abundance, genetic locations, mobility potential, and bacterial hosts within activated sludge relative to those in influent sewage across five WWTPs from three continents. RESULTS The abundances (gene copies per Gb of reads, aka gc/Gb) of all ARGs and those carried by putative pathogens decreased 75-90% from influent sewage (192-605 gc/Gb) to activated sludge (31-62 gc/Gb) at all five WWTPs. Long reads enabled quantification of the percent abundance of ARGs with mobility potential (i.e., located on plasmids or co-located with other mobile genetic elements (MGEs)). The abundance of plasmid-associated ARGs decreased at four of five WWTPs (from 40-73 to 31-68%), and ARGs co-located with transposable, integrative, and conjugative element hallmark genes showed similar trends. Most ARG-associated elements decreased 0.35-13.52% while integrative and transposable elements displayed slight increases at two WWTPs (1.4-2.4%). While resistome and taxonomic compositions both shifted significantly, host phyla for chromosomal ARG classes remained relatively consistent, indicating vertical gene transfer via active biomass growth in activated sludge as the key pathway of chromosomal ARG dissemination. CONCLUSIONS Overall, our results suggest that the activated sludge process acted as a barrier against the proliferation of most ARGs, while those that persisted or increased warrant further attention. Video abstract.
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Affiliation(s)
- Dongjuan Dai
- Department of Civil and Environmental Engineering, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Connor Brown
- Department of Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Helmut Bürgmann
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - D G Joakim Larsson
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Indumathi Nambi
- Department of Civil Engineering, Indian Institute of Technology, Madras, India
| | - Tong Zhang
- Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Carl-Fredrik Flach
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Polytechnic and State University, Blacksburg, VA, USA.
| | - Peter J Vikesland
- Department of Civil and Environmental Engineering, Virginia Polytechnic and State University, Blacksburg, VA, USA.
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