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Ransirini AM, Elżbieta MS, Joanna G, Bartosz K, Wojciech T, Agnieszka B, Magdalena U. Fertilizing drug resistance: Dissemination of antibiotic resistance genes in soil and plant bacteria under bovine and swine slurry fertilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174476. [PMID: 38969119 DOI: 10.1016/j.scitotenv.2024.174476] [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: 03/12/2024] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
The increasing global demand for food production emphasizes the use of organic animal fertilizers, such as manure and slurry, to support sustainable agricultural practices. However, recent studies highlight concerns about antibiotic resistance determinants in animal excrements, posing a potential risk of spreading antibiotic resistance genes (ARGs) in agricultural soil and, consequently, in food products. This study examines the dissemination of ARGs within the soil and plant-associated microbiomes in cherry radish following the application of swine and bovine slurry. In a 45-day pot experiment, slurry-amended soil, rhizospheric bacteria, and endophytic bacteria in radish roots and leaves were sampled and analyzed for 21 ARGs belonging to 7 Antibiotic Resistance Phenotypes (ARPs). The study also assessed slurry's impact on soil microbiome functional diversity, enzymatic activity, physicochemical soil parameters, and the concentration of 22 selected antimicrobials in soil and plant tissues. Tetracyclines and β-lactams were the most frequently identified ARGs in bovine and swine slurry, aligning with similar studies worldwide. Swine slurry showed a higher prevalence of ARGs in soil and plant-associated bacteria, particularly TET genes, reflecting pig antibiotic treatments. The persistent dominance of TET genes across slurry, soil, and plant microbiomes highlights significant influence of slurry application on gene occurrence in plant bacteria. The presence of ARGs in edible plant parts underscores health risks associated with raw vegetable consumption. Time-dependent dynamics of ARG occurrence highlighted their persistent presence throughout the experiment duration, influenced by the environmental factors and antibiotic residuals. Notably, ciprofloxacin, which was the only one antimicrobial detected in fertilized soil, significantly impacted bovine-amended variants. Soil salinity modifications induced by slurry application correlated with changes in ARG occurrence. Overall, the research underscores the complex relationships between agricultural practices, microbial activity, and antibiotic resistance dissemination, emphasizing the need for a more sustainable and health-conscious farming approaches.
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Affiliation(s)
- Attanayake Mudiyanselage Ransirini
- University of Lodz, Faculty of Biology and Environmental Protection, UNESCO Chair on Ecohydrology and Applied Ecology, Banacha 12/16, 90-237 Lodz, Poland
| | - Mierzejewska-Sinner Elżbieta
- University of Lodz, Faculty of Biology and Environmental Protection, UNESCO Chair on Ecohydrology and Applied Ecology, Banacha 12/16, 90-237 Lodz, Poland
| | - Giebułtowicz Joanna
- Medical University of Warsaw, Faculty of Pharmacy, Department of Drug Chemistry, Pharmaceutical and Biomedical Analysis, Banacha 1, 02-097 Warsaw, Poland
| | - Kózka Bartosz
- Medical University of Warsaw, Faculty of Pharmacy, Department of Drug Chemistry, Pharmaceutical and Biomedical Analysis, Banacha 1, 02-097 Warsaw, Poland
| | - Tołoczko Wojciech
- Department of Physical Geography, Faculty of Geography, University of Lodz, Prez. Gabriela Narutowicza 88, 90-139, Lodz, Poland
| | - Bednarek Agnieszka
- University of Lodz, Faculty of Biology and Environmental Protection, UNESCO Chair on Ecohydrology and Applied Ecology, Banacha 12/16, 90-237 Lodz, Poland
| | - Urbaniak Magdalena
- University of Lodz, Faculty of Biology and Environmental Protection, UNESCO Chair on Ecohydrology and Applied Ecology, Banacha 12/16, 90-237 Lodz, Poland.
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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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Yang L, Yu P, Wang J, Zhao T, Zhao Y, Pan Y, Chen L. Genomic and Transcriptomic Analyses Reveal Multiple Strategies for Vibrio parahaemolyticus to Tolerate Sub-Lethal Concentrations of Three Antibiotics. Foods 2024; 13:1674. [PMID: 38890902 PMCID: PMC11171697 DOI: 10.3390/foods13111674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 06/20/2024] Open
Abstract
Vibrio parahaemolyticus can cause acute gastroenteritis, wound infections, and septicemia in humans. The overuse of antibiotics in aquaculture may lead to a high incidence of the multidrug-resistant (MDR) pathogen. Nevertheless, the genome evolution of V. parahaemolyticus in aquatic animals and the mechanism of its antibiotic tolerance remain to be further deciphered. Here, we investigated the molecular basis of the antibiotic tolerance of V. parahaemolyticus isolates (n = 3) originated from shellfish and crustaceans using comparative genomic and transcriptomic analyses. The genome sequences of the V. parahaemolyticus isolates were determined (5.0-5.3 Mb), and they contained 4709-5610 predicted protein-encoding genes, of which 823-1099 genes were of unknown functions. Comparative genomic analyses revealed a number of mobile genetic elements (MGEs, n = 69), antibiotic resistance-related genes (n = 7-9), and heavy metal tolerance-related genes (n = 2-4). The V. parahaemolyticus isolates were resistant to sub-lethal concentrations (sub-LCs) of ampicillin (AMP, 512 μg/mL), kanamycin (KAN, 64 μg/mL), and streptomycin (STR, 16 μg/mL) (p < 0.05). Comparative transcriptomic analyses revealed that there were significantly altered metabolic pathways elicited by the sub-LCs of the antibiotics (p < 0.05), suggesting the existence of multiple strategies for antibiotic tolerance in V. parahaemolyticus. The results of this study enriched the V. parahaemolyticus genome database and should be useful for controlling the MDR pathogen worldwide.
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Affiliation(s)
- Lianzhi Yang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of China, Shanghai 201306, China; (L.Y.); (P.Y.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Pan Yu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of China, Shanghai 201306, China; (L.Y.); (P.Y.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Juanjuan Wang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of China, Shanghai 201306, China; (L.Y.); (P.Y.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Taixia Zhao
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of China, Shanghai 201306, China; (L.Y.); (P.Y.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- College of Tea and Food Science, Wuyi University, Wuyishan 354300, China
| | - Yong Zhao
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of China, Shanghai 201306, China; (L.Y.); (P.Y.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Yingjie Pan
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of China, Shanghai 201306, China; (L.Y.); (P.Y.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of China, Shanghai 201306, China; (L.Y.); (P.Y.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
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Bydalek F, Webster G, Barden R, Weightman AJ, Kasprzyk-Hordern B, Wenk J. Microbial community and antimicrobial resistance niche differentiation in a multistage, surface flow constructed wetland. WATER RESEARCH 2024; 254:121408. [PMID: 38442607 DOI: 10.1016/j.watres.2024.121408] [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: 06/06/2023] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024]
Abstract
Free-living (FL) and particulate-associated (PA) communities are distinct bacterioplankton lifestyles with different mobility and dissemination routes. Understanding spatio-temporal dynamics of PA and FL fractions will allow improvement to wastewater treatment processes including pathogen and AMR bacteria removal. In this study, PA, FL and sediment community composition and antimicrobial resistance gene (ARG; tetW, ermB, sul1, intI1) dynamics were investigated in a full-scale municipal wastewater free-water surface polishing constructed wetland. Taxonomic composition of PA and FL microbial communities shifted towards less diverse communities (Shannon, Chao1) at the CW effluent but retained a distinct fraction-specific composition. Wastewater treatment plant derived PA communities introduced the bulk of AMR load (70 %) into the CW. However, the FL fraction was responsible for exporting over 60 % of the effluent AMR load given its high mobility and the effective immobilization (1-3 log removal) of PA communities. Strong correlations (r2>0.8, p < 0.05) were observed between the FL fraction, tetW and emrB dynamics, and amplicon sequence variants (ASVs) of potentially pathogenic taxa, including Bacteroides, Enterobacteriaceae, Aeromonadaceae, and Lachnospiraceae. This study reveals niche differentiation of microbial communities and associated AMR in CWs and shows that free-living bacteria are a primary escape route of pathogenic and ARG load from CWs under low-flow hydraulic conditions.
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Affiliation(s)
- Franciszek Bydalek
- Department of Chemical Engineering, University of Bath, Claverton Down, Bath BA2 7AY, UK; Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK; GW4 NERC CDT in Freshwater Biosciences and Sustainability, Cardiff University, Cardiff CF10 3AX, UK; Organisms and Environment Division, School of Biosciences, Microbiomes, Microbes and Informatics Group, Cardiff University, Cardiff CF10 3AX, UK
| | - Gordon Webster
- Organisms and Environment Division, School of Biosciences, Microbiomes, Microbes and Informatics Group, Cardiff University, Cardiff CF10 3AX, UK
| | | | - Andrew J Weightman
- Organisms and Environment Division, School of Biosciences, Microbiomes, Microbes and Informatics Group, Cardiff University, Cardiff CF10 3AX, UK
| | - Barbara Kasprzyk-Hordern
- Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK; Department of Chemistry, University of Bath, Bath BA2 7AY, UK
| | - Jannis Wenk
- Department of Chemical Engineering, University of Bath, Claverton Down, Bath BA2 7AY, UK; Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK.
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Ota Y, Prah I, Mahazu S, Gu Y, Nukui Y, Koike R, Saito R. Novel insights into genetic characteristics of blaGES-encoding plasmids from hospital sewage. Front Microbiol 2023; 14:1209195. [PMID: 37664110 PMCID: PMC10469963 DOI: 10.3389/fmicb.2023.1209195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction The prevalence of Guiana extended-spectrum (GES)-type carbapenemase producers is increasing worldwide, and hospital water environments are considered as potential reservoirs. However, the genetic features underlying this resistance are not yet fully understood. This study aimed to characterize blaGES-encoding plasmids from a single-hospital sewage sample in Japan. Methods Carbapenemase producers were screened using carbapenemase-selective agar and polymerase chain reaction. Whole-genome sequencing analyzes were performed on the carbapenemase-producing isolates. Results Eleven gram-negative bacteria (four Enterobacter spp., three Klebsiella spp., three Aeromonas spp., and one Serratia spp.) with blaGES-24 (n = 6), blaGES-6 (n = 4), and blaGES-5 (n = 1) were isolated from the sewage sample. Five blaGES-24 and a blaGES-5 were localized in IncP-6 plasmids, whereas three blaGES-6 plasmids were localized in IncC plasmids with IncF-like regions. The remaining blaGES-6 and blaGES-24 were, respectively, localized on IncFIB-containing plasmids with IncF-like regions and a plasmid with an IncW-like replication protein. The IncP-6 and IncW-like plasmids had a close genetic relationship with plasmids from Japan, whereas the IncC/IncF-like and IncFIB/IncF-like plasmids were closely related to those from the United States and Europe. All blaGES genes were located on the class 1 integron cassette of the Tn3 transposon-related region, and the IncC/IncF-like plasmid carried two copies of the integron cassette. Eight of the eleven blaGES-encoding plasmids contained toxin-antitoxin system genes. Discussion The findings on the plasmids and the novel genetic content from a single wastewater sample extend our understanding regarding the diversity of resistance and the associated spread of blaGES, suggesting their high adaptability to hospital effluents. These findings highlight the need for the continuous monitoring of environmental GES-type carbapenemase producers to control their dissemination.
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Affiliation(s)
- Yusuke Ota
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Isaac Prah
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Samiratu Mahazu
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Parasitology and Tropical Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshiaki Gu
- Department of Infectious Diseases, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoko Nukui
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryuji Koike
- Clinical Research Center, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| | - Ryoichi Saito
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
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Liu Z, Wan X, Zhang C, Cai M, Pan Y, Li M. Deep sequencing reveals comprehensive insight into the prevalence, mobility, and hosts of antibiotic resistance genes in mangrove ecosystems. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 335:117580. [PMID: 36857890 DOI: 10.1016/j.jenvman.2023.117580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/13/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Mangrove receives aquaculture wastewater and urban sewage, and thus is a potential reservoir for antibiotic resistance genes (ARGs). However, there is a dearth of a comprehensive profile of ARGs in mangrove ecosystems. We used metagenomic techniques to uncover the occurrence, host range, and potential mobility of ARGs in six mangrove ecosystems in southeastern China. Based on deep sequencing data, a total of 348 ARG subtypes were identified. The abundant ARGs were associated with acriflavine, bacitracin, beta-lactam, fluoroquinolone, macrolide-lincosamide-streptogramin, and polymyxin. Resistance genes tetR, aac(6')-Iae, aac(3)-IXa, vanRA, vanRG, and aac(3)-Ig were proposed as ARG indicators in mangrove ecosystems that can be used to evaluate the abundance of 100 other co-occurring ARGs quantitatively. Remarkably, 250 of 348 identified ARG subtypes were annotated as mobile genetic elements-associated ARGs, indicating a high potential risk of propagation of ARGs in mangrove ecosystems. By surveying the distribution of ARGs in 6281 draft genomes, more than 42 bacterial phyla were identified as the putative hosts of the ARGs. Among them, 21.97% were potentially multidrug-resistant hosts, including human and animal opportunistic pathogens. This research adds to our understanding of the distribution and spread of antibiotic resistomes in mangrove ecosystems, helping improve ARG risk assessment and management worldwide.
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Affiliation(s)
- Zongbao Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China; Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Xiulin Wan
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China
| | - Cuijing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Mingwei Cai
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Yueping Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China.
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Li S, Gao H, Zhang H, Wei G, Shu Q, Li R, Jin S, Na G, Shi Y. The fate of antibiotic resistance genes in the coastal lagoon with multiple functional zones. J Environ Sci (China) 2023; 128:93-106. [PMID: 36801045 DOI: 10.1016/j.jes.2022.07.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 06/18/2023]
Abstract
Coastal lagoons provide many important services to human society, but their year-round use for aquaculture introduces large amounts of sewage. The contamination of antibiotic resistance genes (ARGs) is therefore of great concern. In this study, 50 ARGs subtypes, two integrase genes (intl1, intl2), and 16S rRNA genes were detected by high-throughput quantitative PCR, and standard curves of all target genes were prepared for quantification. The occurrence and distribution of ARGs in a typical coastal lagoon (XinCun lagoon, China) were comprehensively explored. We detected 44 and 38 subtypes of ARGs in the water and sediment, respectively, and discuss the various factors influencing the fate of ARGs in the coastal lagoon. Macrolides-lincosamides-streptogramins B was the primary ARG type, and macB was the predominant subtype. Antibiotic efflux and antibiotic inactivation were the main ARG resistance mechanisms. The XinCun lagoon was divided into eight functional zones. The ARGs showed a distinct spatial distribution owing to the influence of microbial biomass and anthropogenic activity in different functional zones. Fishing rafts, abandoned fish ponds, the town sewage zone, and mangrove wetlands provided a large quantity of ARGs to the XinCun lagoon. Nutrients and heavy metals also significantly correlated with the fate of the ARGs, especially NO2--N and Cu, which cannot be ignored. It is noteworthy that lagoon-barrier systems coupled with persistent pollutant inputs result in coastal lagoons acting as a "buffer pool" for ARGs, which can then accumulate and threaten the offshore environment.
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Affiliation(s)
- Shisheng Li
- National Marine Environmental Monsitoring Center, Dalian 116023, China; College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Hui Gao
- National Marine Environmental Monsitoring Center, Dalian 116023, China
| | - Haibo Zhang
- National Marine Environmental Monsitoring Center, Dalian 116023, China
| | - Guangke Wei
- Laboratory for coastal marine eco-environment process and carbon sink of Hainan provincet/Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya 572022, China
| | - Qin Shu
- National Marine Environmental Monsitoring Center, Dalian 116023, China; College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Ruijing Li
- National Marine Environmental Monsitoring Center, Dalian 116023, China
| | - Shuaichen Jin
- National Marine Environmental Monsitoring Center, Dalian 116023, China
| | - Guangshui Na
- Laboratory for coastal marine eco-environment process and carbon sink of Hainan provincet/Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya 572022, China; National Marine Environmental Monsitoring Center, Dalian 116023, China; College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China.
| | - Yali Shi
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.
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Yang K, Chen ML, Zhu D. Exposure to benzalkonium chloride disinfectants promotes antibiotic resistance in sewage sludge microbiomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161527. [PMID: 36638983 PMCID: PMC9830840 DOI: 10.1016/j.scitotenv.2023.161527] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/27/2022] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
Disinfectants are routinely used in human environments to control and prevent the transmission of microbial disease, and this is particularly true during the current COVID-19 crisis. However, it remains unclear whether the increased disinfectant loadings to wastewater treatment plants facilitate the dissemination of antibiotic resistance genes (ARGs) in sewage sludge microbiomes. Here, we investigated the impacts of benzalkonium chlorides (BACs), widely used disinfectants, on ARGs profiles and microbial community structures in sewage sludge by using high-throughput quantitative PCR and Illumina sequencing. A total of 147 unique ARGs and 39 mobile genetic elements (MGEs) were detected in all sewage sludge samples. Our results show that exposure to BACs disinfectants at environmentally relevant concentrations significantly promotes both the diversity and absolute abundance of ARGs in sludge microbiomes, indicating the co-selection of ARGs by BACs disinfectants. The enrichment of ARGs abundance varied from 2.15-fold to 3.63-fold compared to controls. In addition, BACs exposure significantly alters bacterial and protistan communities, resulting in dysbiosis of the sludge microbiota. The Mantel test and Procrustes analysis confirm that bacterial communities are significantly correlated with ARGs profiles under BACs treatments. The structural equation model explains 83.8 % of the total ARGs variation and further illustrates that the absolute abundance of MGEs exerts greater impacts on the variation of absolute abundance of ARGs than microbial communities under BACs exposure, suggesting BACs may promote antibiotic resistance by enhancing the horizontal gene transfer of ARGs across sludge microbiomes. Collectively, our results provide new insights into the proliferation of antibiotic resistance through disinfectant usage during the pandemic and highlight the necessity to minimize the environmental release of disinfectants into the non-target environment for combating antibiotic resistance.
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Affiliation(s)
- Kai Yang
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Mo-Lian Chen
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo 315800, China
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Matviichuk O, Mondamert L, Geffroy C, Dagot C, Labanowski J. Life in an unsuspected antibiotics world: River biofilms. WATER RESEARCH 2023; 231:119611. [PMID: 36716569 DOI: 10.1016/j.watres.2023.119611] [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: 08/23/2022] [Revised: 12/20/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Waterborne bacteria that naturally live in biofilms are continuously exposed to pharmaceutical residues, regularly released into the freshwater environment. At the source level, the discharge of antibiotics into rivers has already been repeatedly linked to the development of antimicrobial resistance. But what about biofilms away from the discharge point? Two rivers, with sites subject to dispersed contamination of medium intensity, were studied as typical representatives of high- and middle-income countries. The biofilms developed on rocks indigenous to rivers are perfectly representative of environmental exposure. Our results show that away from the hotspots, the amount of antibiotics in the biofilms studied favours the maintenance and enrichment of existing resistant strains as well as the selection of new resistant mutants, and these favourable conditions remain over a period of time. Thus, in this type of river, the environmental risk of selection pressure is not only present downstream of urbanized areas but is also possible upstream and far downstream of wastewater treatment plant discharges. Despite this, correlation analysis found no strong positive correlation between antibiotic concentrations and the abundance of measured integrons and their corresponding resistance genes. Nevertheless, this work highlights the need to consider the risks of antibiotics beyond hotspots as well.
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Affiliation(s)
- Olha Matviichuk
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, France; University of Limoges, Inserm, CHU Limoges, RESINFIT, U 1092, F-87000 Limoges, France
| | - Leslie Mondamert
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, France
| | - Claude Geffroy
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, France
| | - Christophe Dagot
- University of Limoges, Inserm, CHU Limoges, RESINFIT, U 1092, F-87000 Limoges, France
| | - Jérôme Labanowski
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, France.
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An R, Qi Y, Zhang XX, Ma L. Xenogenetic evolutionary of integrons promotes the environmental pollution of antibiotic resistance genes - Challenges, progress and prospects. WATER RESEARCH 2023; 231:119629. [PMID: 36689882 DOI: 10.1016/j.watres.2023.119629] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/18/2022] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
Environmental pollution of antibiotic resistance genes (ARGs) has been a great public concern. Integrons, as mobile genetic elements, with versatile gene acquisition systems facilitate the horizontal gene transfer (HGT) and pollution disseminations of ARGs. However, little is understood about the characteristics of ARGs mediated by integrons, which hampers our monitoring and control of the mobile antimicrobial resistance risks. To address these issues, we reviewed 3,322 publications concerning detection methods and pipeline, ARG diversity and evolutionary progress, environmental and geographical distribution, bacterial hosts, gene cassettes arrangements, and based on which to identify ARGs with high risk levels mediated by integrons. Diverse ARGs of 516 subtypes attributed to 12 types were capable of being carried by integrons, with 62 core ARG subtypes prevalent in pollution source, natural and human-related environments. Hosts of ARG-carrying integrons reached 271 bacterial species, most frequently carried by opportunistic pathogens Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae. Moreover, the observed emergence of ARGs together with their multiple arrangements indicated the accumulation of ARGs mediated by integrons, and thus pose increasing HGT risks under modern selective agents. With the concerns of public health, we urgently call for a better monitoring and control of these high-risk ARGs. Our identified Risk Rank I ARGs (aacA7, blaOXA10, catB3, catB8, dfrA5) with high mobility, reviewed key trends and noteworthy advancements, and proposed future directions could be reference and guidance for standard formulation.
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Affiliation(s)
- Ran An
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Yuting Qi
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Liping Ma
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China.
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11
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Shukla R, Ahammad SZ. Performance assessment of a modified trickling filter and conventional activated sludge process along with tertiary treatment in removing emerging pollutants from urban sewage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159833. [PMID: 36374754 DOI: 10.1016/j.scitotenv.2022.159833] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
The absence of effective wastewater treatment technology to eliminate emerging pollutants from municipal sewage has become a pressing issue. In this study, the efficacy of a novel modified trickling filter (MTF), conventional activated sludge process (ASP) and two tertiary systems (UV and ozonation) were compared in eliminating antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs) and pharmaceuticals and personal care products (PPCPs) from urban sewage. MTF and ASP resulted in >1 log unit reduction in the abundance of ARB, while for ARGs, the removal was observed in the range of 0.1 to 1.7 log units. In MTF, ARGs were substantially removed in the aerobic zone compared to the anoxic zone. The relative abundance of most of the ARGs either decreased or remained unchanged during MTF and ASP operations. However, the relative abundance of most of the ARGs increased in the secondary sludge generated from ASP. The concentration of PPCPs such as atenolol, sulfamethazine, triclosan, and ranitidine was reduced by MTF by >80 %. Overall, the results indicated that MTF followed by ozonation is the most effective combination for removing emerging contaminants from municipal sewage.
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Affiliation(s)
- Rishabh Shukla
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shaikh Ziauddin Ahammad
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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12
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Zhao CX, Su XX, Xu MR, An XL, Su JQ. Uncovering the diversity and contents of gene cassettes in class 1 integrons from the endophytes of raw vegetables. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 247:114282. [PMID: 36371907 DOI: 10.1016/j.ecoenv.2022.114282] [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: 07/11/2022] [Revised: 10/22/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Rapid spread of antibiotic resistance genes (ARGs) in pathogens is threatening human health. Integrons allow bacteria to integrate and express foreign genes, facilitating horizontal transfer of ARGs in environments. Consumption of raw vegetables represents a pathway for human exposure to environmental ARGs. However, few studies have focused on integron-associated ARGs in the endophytes of raw vegetables. Here, based on the approach of qPCR and clone library, we quantified the abundance of integrase genes and analyzed the diversity and contents of resistance gene cassettes in class 1 integrons from the endophytes of six common raw vegetables. The results revealed that integrase genes for class 1 integron were most prevalent compared with class 2 and class 3 integron integrase genes (1-2 order magnitude, P < 0.05). The cucumber endophytes harbored a higher absolute abundance of integrase genes than other vegetables, while the highest bacterial abundance was detected in cabbage and cucumber endophytes. Thirty-two unique resistance gene cassettes were detected, the majority of which were associated with the genes encoding resistance to beta-lactam and aminoglycoside. Antibiotic resistance gene cassettes accounted for 52.5 % of the functionally annotated gene cassettes, and blaTEM-157 and aadA2 were the most frequently detected resistance cassettes. Additionally, carrot endophytes harbored the highest proportion of antibiotic resistance gene cassettes in the class 1 integrons. Collectively, these results provide an in-depth view of acquired resistance genes by integrons in the raw vegetable endophytes and highlight the potential health risk of the transmission of ARGs via the food chain.
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Affiliation(s)
- Cai-Xia Zhao
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Xuan Su
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, 400715 Chongqing, China
| | - Mei-Rong Xu
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Li An
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jian-Qiang Su
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Genomic and Transcriptomic Analysis Reveal Multiple Strategies for the Cadmium Tolerance in Vibrio parahaemolyticus N10-18 Isolated from Aquatic Animal Ostrea gigas Thunberg. Foods 2022; 11:foods11233777. [PMID: 36496584 PMCID: PMC9741282 DOI: 10.3390/foods11233777] [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: 09/17/2022] [Revised: 11/05/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022] Open
Abstract
The waterborne Vibrio parahaemolyticus can cause acute gastroenteritis, wound infection, and septicemia in humans. Pollution of heavy metals in aquatic environments is proposed to link high incidence of the multidrug-resistant (MDR) pathogen. Nevertheless, the genome evolution and heavy metal tolerance mechanism of V. parahaemolyticus in aquatic animals remain to be largely unveiled. Here, we overcome the limitation by characterizing an MDR V. parahaemolyticus N10-18 isolate with high cadmium (Cd) tolerance using genomic and transcriptomic techniques. The draft genome sequence (4,910,080 bp) of V. parahaemolyticus N10-18 recovered from Ostrea gigas Thunberg was determined, and 722 of 4653 predicted genes had unknown function. Comparative genomic analysis revealed mobile genetic elements (n = 11) and heavy metal and antibiotic-resistance genes (n = 38 and 7). The bacterium significantly changed cell membrane structure to resist the Cd2+ (50 μg/mL) stress (p < 0.05). Comparative transcriptomic analysis revealed seven significantly altered metabolic pathways elicited by the stress. The zinc/Cd/mercury/lead transportation and efflux and the zinc ATP-binding cassette (ABC) transportation were greatly enhanced; metal and iron ABC transportation and thiamine metabolism were also up-regulated; conversely, propanoate metabolism and ribose and maltose ABC transportation were inhibited (p < 0.05). The results of this study demonstrate multiple strategies for the Cd tolerance in V. parahaemolyticus.
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14
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Zhang Y, Su YA, Qiu X, Mao Q, Liu H, Liu H, Wen D, Su Z. Temperature affects variations of class 1 integron during sludge anaerobic digestion. BIORESOURCE TECHNOLOGY 2022; 364:128005. [PMID: 36155808 DOI: 10.1016/j.biortech.2022.128005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Revealing class 1 integron characteristics under different operating conditions is of great importance to control antibiotic resistance genes (ARGs) during sludge anaerobic digestion (AD). This study investigated the variations of class 1 integrons and the ARGs carried by class 1 integrons in anaerobic sludge digesters under 25 °C, 35 °C, and 55 °C. The results showed lower intI1 abundance and fewer class I integrons with long gene cassette arrays at 55 °C than at 25 °C and 35 °C. Multi-resistance gene cassette arrays were observed in the digesters at 25 °C and 35 °C. Abundant ARGs were detected on class 1 integrons in all digesters with aminoglycosides as the dominant class. The abundance of ARGs on class 1 integrons in digesters at 55 °C was lower than that at 25 °C and 35 °C. Thermophilic AD is better than mesophilic ones in the control of ARGs carried by class 1 integrons.
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Affiliation(s)
- Yan Zhang
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Water Treatment Technology and Material, Suzhou 215011, China
| | - Yu-Ao Su
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Xuyang Qiu
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Qiuyan Mao
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Hongbo Liu
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Water Treatment Technology and Material, Suzhou 215011, China
| | - He Liu
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Water Treatment Technology and Material, Suzhou 215011, China.
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhiguo Su
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
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15
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Burata OE, Yeh TJ, Macdonald CB, Stockbridge RB. Still rocking in the structural era: A molecular overview of the small multidrug resistance (SMR) transporter family. J Biol Chem 2022; 298:102482. [PMID: 36100040 PMCID: PMC9574504 DOI: 10.1016/j.jbc.2022.102482] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/24/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022] Open
Abstract
The small multidrug resistance (SMR) family is composed of widespread microbial membrane proteins that fulfill different transport functions. Four functional SMR subtypes have been identified, which variously transport the small, charged metabolite guanidinium, bulky hydrophobic drugs and antiseptics, polyamines, and glycolipids across the membrane bilayer. The transporters possess a minimalist architecture, with ∼100-residue subunits that require assembly into homodimers or heterodimers for transport. In part because of their simple construction, the SMRs are a tractable system for biochemical and biophysical analysis. Studies of SMR transporters over the last 25 years have yielded deep insights for diverse fields, including membrane protein topology and evolution, mechanisms of membrane transport, and bacterial multidrug resistance. Here, we review recent advances in understanding the structures and functions of SMR transporters. New molecular structures of SMRs representing two of the four functional subtypes reveal the conserved structural features that have permitted the emergence of disparate substrate transport functions in the SMR family and illuminate structural similarities with a distantly related membrane transporter family, SLC35/DMT.
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Affiliation(s)
- Olive E Burata
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Trevor Justin Yeh
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Randy B Stockbridge
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA; Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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16
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The Resistome of ESKAPEE Pathogens in Untreated and Treated Wastewater: A Polish Case Study. Biomolecules 2022; 12:biom12081160. [PMID: 36009054 PMCID: PMC9405806 DOI: 10.3390/biom12081160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to quantify ESKAPEE bacteria, genes encoding resistance to antibiotics targeting this group of pathogens, as well as integrase genes in municipal wastewater and river water. Environmental DNA was extracted from the collected samples and used in deep sequencing with the Illumina TruSeq kit. The abundance of bacterial genera and species belonging to the ESKAPEE group, 400 ARGs associated with this microbial group, and three classes of integrase genes were determined. A taxonomic analysis revealed that Acinetobacter was the dominant bacterial genus, whereas Acinetobacter baumannii and Escherichia coli were the dominant bacterial species. The analyzed samples were characterized by the highest concentrations of the following ARGs: blaGES, blaOXA-58, blaTEM, qnrB, and qnrS. Acinetobacter baumannii, E. coli, and genes encoding resistance to β-lactams (blaVEB-1, blaIMP-1, blaGES, blaOXA-58, blaCTX-M, and blaTEM) and fluoroquinolones (qnrS) were detected in samples of river water collected downstream from the wastewater discharge point. The correlation analysis revealed a strong relationship between A. baumannii (bacterial species regarded as an emerging human pathogen) and genes encoding resistance to all tested groups of antimicrobials. The transmission of the studied bacteria (in particular A. baumannii) and ARGs to the aquatic environment poses a public health risk.
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17
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Li HZ, Zhu D, Sun AQ, Qin YF, Lindhardt JH, Cui L. Effects of soil protists on the antibiotic resistome under long term fertilization. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119516. [PMID: 35609845 DOI: 10.1016/j.envpol.2022.119516] [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: 11/12/2021] [Revised: 05/09/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Soil protists are key in regulating soil microbial communities. However, our understanding on the role of soil protists in shaping antibiotic resistome is limited. Here, we considered the diversity and composition of bacteria, fungi and protists in arable soils collected from a long-term field experiment with multiple fertilization treatments. We explored the effects of soil protists on antibiotic resistome using high-throughput qPCR. Our results showed that long term fertilization had stronger effect on the composition of protists than those of bacteria and fungi. The detected number and relative abundance of antibiotic resistance genes (ARGs) were elevated in soils amended with organic fertilizer. Co-occurrence network analysis revealed that changes in protists may contribute to the changes in ARGs composition, and the application of different fertilizers altered the communities of protistan consumers, suggesting that effects of protistan communities on ARGs might be altered by the top-down impact on bacterial composition. This study demonstrates soil protists as promising agents in monitoring and regulating ecological risk of antibiotic resistome associated with organic fertilizers.
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Affiliation(s)
- Hong-Zhe Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - An-Qi Sun
- Key Laboratory for Humid Subtropical Ecogeographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Yi-Fei Qin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Jonathan Hessner Lindhardt
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871, Frederiksberg, Denmark; Sino-Danish Center for Education and Research, Beijing, China
| | - Li Cui
- 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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18
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Usui M, Tamura Y, Asai T. Current status and future perspective of antimicrobial-resistant bacteria and resistance genes in animal-breeding environments. J Vet Med Sci 2022; 84:1292-1298. [PMID: 35871558 PMCID: PMC9523292 DOI: 10.1292/jvms.22-0253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The emergence and spread of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs) are a global public health concern. ARB are transmitted directly or indirectly
from animals to humans. The importance of environmental transmission of ARB and ARGs has recently been demonstrated, given the relationships between compost, livestock wastewater, insects,
and wildlife. In addition, companion animals and their surrounding environments (veterinary hospitals and homes with companion animals) should be considered owing to their close relationship
with humans. This review discusses the current status and future perspectives of ARB and ARGs in animal-breeding environments.
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Affiliation(s)
- Masaru Usui
- Laboratory of Food Microbiology and Food Safety, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University
| | - Yutaka Tamura
- Laboratory of Food Microbiology and Food Safety, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University
| | - Tetsuo Asai
- Department of Applied Veterinary Science, The United Graduate School of Veterinary Science, Gifu University
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19
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Ping Q, Zhang Z, Ma L, Yan T, Wang L, Li Y. The prevalence and removal of antibiotic resistance genes in full-scale wastewater treatment plants: Bacterial host, influencing factors and correlation with nitrogen metabolic pathway. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154154. [PMID: 35245555 DOI: 10.1016/j.scitotenv.2022.154154] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
This study investigated the prevalence of antibiotic resistance genes (ARGs) in the influent, effluent, and waste activated sludge (WAS) of eight full-scale municipal wastewater treatment plants (WWTPs) in Shanghai, China. A comprehensive understanding of the correlation between various influencing factors (characteristics of wastewater and WAS, antibiotics, metals, mobile genetic elements) and ARGs was explored. Among the eight full-scale WWTPs, the Unitank process was inefficient in removing typical ARGs compared with continuous-flow anaerobic-anoxic-aerobic and oxidation ditch processes. Antibiotic was identified as the most influential factor affecting the occurrence of ARGs in wastewater, followed by flow rate and nutrients. Positive correlations were observed between antibiotics and their corresponding ARGs in the influent, while this correlation disappeared in the WAS. Class I integron, wastewater characteristics (nitrogen and flow rate), antibiotics (ofloxacin, sulfamethazine, and erythromycin), metals (Mg, Al, Fe, and Mn) were identified as crucial factors comprehensively affecting the distribution of ARGs in WAS. Dissimilatory nitrate reduction profoundly influenced the fate of ARGs during wastewater treatment processes, and K04561 (norB), K02567 (napA), K00262 (gdhA), K00284 (gltS) were identified as the most significant genes in the nitrogen metabolism pathway (ko00910). This study provides a new perspective for comprehensively understanding the occurrence and dissemination of ARGs in WWTPs.
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Affiliation(s)
- Qian Ping
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Zhipeng Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Liping Ma
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Tingting Yan
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Lin Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Yongmei Li
- State Key Laboratory of Pollution Control and Resource Reuse, 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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20
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Tansirichaiya S, Winje E, Wigand J, Al-Haroni M. Inverse PCR-based detection reveal novel mobile genetic elements and their associated genes in the human oral metagenome. BMC Oral Health 2022; 22:210. [PMID: 35624467 PMCID: PMC9137128 DOI: 10.1186/s12903-022-02209-y] [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: 12/09/2021] [Accepted: 05/03/2022] [Indexed: 11/20/2022] Open
Abstract
The human oral cavity is one of the hotspots harboring multiple mobile genetic elements (MGEs), which are segments of DNA that can move either within bacterial genomes or between bacterial cells that can facilitate the spreading of genetic materials, including antimicrobial resistance genes. It is, therefore, important to investigate genes associated with the MGEs as they have a high probability of dissemination within the bacterial population under selective pressure from human activities. As one-third of oral bacteria are not yet culturable in the laboratory condition, therefore, in this work, it is aimed to detect and identify the genetic contexts of MGEs in the oral cavity through an inverse PCR (IPCR)-based approach on the oral metagenomic. The human oral metagenome was extracted from saliva samples collected from healthy individuals in Tromsø, Norway. The extracted DNA was partially digested with the HindIII restriction enzyme and self-circularized by ligation. DNA primers targeting each MGE were designed to amplify outwards from the MGEs and used for the IPCR on the circularized DNA products. The IPCR amplicons were cloned into a pCR-XL-2-TOP vector, screened, and sequenced. Out of 40 IPCR amplicons, we confirmed and verified the genetic contexts of 11 samples amplified with primers targeting integron gene cassettes (GCs), IS431 composite transposons, and Tn916 conjugative transposons (tet(M) and xis-int). Novel integron GCs, MGEs, and variants of Tn916 conjugative transposons were identified, which is the first report using the IPCR technique to detect the genetic contexts of MGEs in the oral metagenomic DNA.
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Affiliation(s)
- Supathep Tansirichaiya
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway
- Centre for New Antimicrobial Strategies, UiT the Arctic University of Norway, Tromsø, Norway
| | - Endre Winje
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway
| | - Johannes Wigand
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway
| | - Mohammed Al-Haroni
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway.
- Centre for New Antimicrobial Strategies, UiT the Arctic University of Norway, Tromsø, Norway.
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21
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Selvaraj GK, Wang H, Zhang Y, Tian Z, Chai W, Lu H. Class 1 In-Tn5393c array contributed to antibiotic resistance of non-pathogenic Pseudoxanthomonas mexicana isolated from a wastewater bioreactor treating streptomycin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153537. [PMID: 35101502 DOI: 10.1016/j.scitotenv.2022.153537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/23/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
The emergence of antibiotic resistance in retort to environmental pollutants during wastewater treatment still remains elusive. Here, we first to investigate the emergence of antibiotic resistance in an environmental non-pathogenic bacterium, Pseudoxanthomonas mexicana isolated from a lab-scale bioreactor treating wastewater containing streptomycin. The molecular mechanism of antibiotic resistance development was evaluated in its genomic, transcriptional, and proteomic levels. The streptomycin resistant (SR) strain showed strong resistance to streptomycin (MIC > 600 μg/mL) as well to sulfamethoxazole, ampicillin, and kanamycin (≥250 μg/mL). A 13.4 kb class-1-integron array consisting of a new arrangement of gene cassette (IS6100-sul1-aadA2-catB3-aacA1-2-aadB-int1-IS256-int) linked with Tn5393c transposon was identified in the SR strain, which has only been reported in clinical pathogens so far. iTRAQ-LC-MS/MS proteomics revealed 22 up-regulated proteins in the SR strain growing under 100 mg L-1 streptomycin, involving antibiotic resistance, toxin production, stress response, and ribosomal protein synthesis. At the mRNA level, elevated expressions of ARGs (strA, strB, and aadB) and 30S-ribosomal protein genes (rpsA and rpsU) were observed in the SR strain. The results highlighted the genomic plasticity and multifaceted regulatory mechanism employed by P. mexicana in adaptation to high-level streptomycin during biological wastewater treatment.
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Affiliation(s)
- Ganesh-Kumar Selvaraj
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Department of Microbiology, St. Peter's Institute of Higher Education and Research, Chennai 600054, Tamil Nadu, India
| | - Hanqing Wang
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhe Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wenbo Chai
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huijie Lu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Zou Y, Wu M, Liu J, Tu W, Xie F, Wang H. Deciphering the extracellular and intracellular antibiotic resistance genes in multiple environments reveals the persistence of extracellular ones. JOURNAL OF HAZARDOUS MATERIALS 2022; 429:128275. [PMID: 35093750 DOI: 10.1016/j.jhazmat.2022.128275] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/18/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
The extracellular and intracellular antibiotic resistance genes (eARGs and iARGs) together constitute the entire resistome in environments. However, the systematic analysis of eARGs and iARGs was still inadequate. Three kinds of environments, i.e., livestock manure, sewage sludge, and lake sediment, were analyzed to reveal the comprehensive characteristics of eARGs and iARGs. Based on the metagenomic data, the diversities, relative abundances, and compositions of eARGs and iARGs were similar. The extracellular and intracellular integrons and insertion sequences (ISs) also did not show any significant differences. However, the degree and significance of the correlation between total relative abundances of integrons/ISs and ARGs were lower outside than inside the cells. Gene cassettes carried by class 1 integron were amplified in manure and sludge samples, and sequencing results showed that the identified ARGs extracellularly and intracellularly were distinct. By analyzing the genetic contexts, most ARGs were found located on chromosomes. Nevertheless, the proportion of ARGs carried by plasmids increased extracellularly. qPCR was employed to quantify the absolute abundances of sul1, sul2, tetO, and tetW, and their extracellular proportions were found highest in sludge samples. These findings together raised the requirements of considering eARGs and iARGs separately in terms of risk evaluation and removal management.
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Affiliation(s)
- Yina Zou
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Menghan Wu
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiayu Liu
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Weiming Tu
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Fengxing Xie
- Tianjin Institute of Agricultural Resources and Environment, Tianjin Academy of Agricultural Science, Tianjin 300384, China
| | - Hui Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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23
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Dias MF, Leroy-Freitas D, Machado EC, da Silva Santos L, Leal CD, da Rocha Fernandes G, de Araújo JC. Effects of activated sludge and UV disinfection processes on the bacterial community and antibiotic resistance profile in a municipal wastewater treatment plant. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:36088-36099. [PMID: 35060061 DOI: 10.1007/s11356-022-18749-3] [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: 07/21/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Wastewater tertiary treatment has been pointed out as an effective alternative for reducing the concentration of antibiotic resistant bacteria and genes (ARB and ARGs) in wastewaters. The present work aimed to build on the current knowledge about the effects of activated sludge and UV irradiation on antibiotic resistance determinants in biologically treated wastewaters. For that, the microbial community and ARGs' composition of samples collected after preliminary (APT), secondary (AST), and tertiary (ATT) treatments in a full-scale wastewater treatment plant using a modified activated sludge (MAS) system followed by an UV stage (16 mJ/cm2) were investigated through culture-dependent and independent approaches (including metagenomics). A total of 24 phyla and 460 genera were identified, with predominance of Gammaproteobacteria in all samples. Pathogenic genera corresponded to 8.6% of all sequences on average, mainly Acinetobacter and Streptococcus. Significant differences (p < 0.05) in the proportion of pathogens were observed between APT and the other samples, suggesting that the secondary treatment reduced its abundance. The MAS achieved 64.0-99.7% average removal efficiency for total (THB) and resistant heterotrophic bacteria, although the proportions of ARB/THB have increased for sulfamethoxazole, cephalexin, ciprofloxacin, and tetracycline. A total of 107 copies/mL of intI1 gene remained in the final effluent, suggesting that the treatment did not significantly remove this gene and possibly other ARGs. In accordance, metagenomic results suggested that number of reads recruited to plasmid-associated ARGs became more abundant in the pool throughout the treatment, suggesting that it affected more the bacteria without these ARGs than those with it. In conclusion, disinfected effluents are still a potential source for ARB and ARGs, which highlights the importance to investigate ways to mitigate their release into the environment.
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Affiliation(s)
- Marcela França Dias
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901, Brazil
| | - Deborah Leroy-Freitas
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901, Brazil
| | - Elayne Cristina Machado
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901, Brazil
| | - Leticia da Silva Santos
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901, Brazil
| | - Cintia Dutra Leal
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901, Brazil
| | | | - Juliana Calábria de Araújo
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901, Brazil.
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24
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An XL, Abass OK, Zhao CX, Xu MR, Pan T, Pu Q, Liao H, Li H, Zhu YG, Su JQ. Nanopore sequencing analysis of integron gene cassettes in sewages and soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 817:152766. [PMID: 35007603 DOI: 10.1016/j.scitotenv.2021.152766] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/23/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
Integrons are genetic elements that can facilitate rapid spread of antibiotic resistance by insertion and removal of genes. However, knowledge about the diversity and distribution of gene cassettes embedded in class 1 integron is still limited. In this study, we sequenced integron gene cassettes using nanopore sequencing and quantified antibiotic resistance genes (ARGs) and integrase genes in the manured soils and sewages of a bioreactor. The results showed that class 1 integron integrase genes were the most abundant in soils and sewages compared with class 2 and class 3 integrase genes. Long-term manure application exacerbated the enrichment of total ARGs, integrase genes and antibiotic resistance-associated gene cassettes, while antibiotics and heavy metals showed no impact on the overall resistome profile. Sewage treatment could efficiently remove the absolute abundance of integrase genes (~3 orders of magnitude, copies/L) and antibiotic resistance gene cassettes. The resistance gene cassettes mainly carried the ARGs conferring resistance to aminoglycoside and beta-lactams in soils and sewages, some of which were persistent during the sewage treatment. This study underlined that soil and sewage were potential reservoirs for integron-mediated ARGs transfer, indicating that anthropogenic activity played a vital role in the prevalence and diversity of resistance gene cassettes in integrons.
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Affiliation(s)
- Xin-Li An
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Olusegun K Abass
- School of Civil and Environmental Engineering, Nanyang Technological University, Nanyang Avenue, 639798, Singapore
| | - Cai-Xia Zhao
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mei-Rong Xu
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Ting Pan
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Pu
- Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Hu Liao
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hu Li
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yong-Guan Zhu
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory 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; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Qiang Su
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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25
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Jankowski P, Gan J, Le T, McKennitt M, Garcia A, Yanaç K, Yuan Q, Uyaguari-Diaz M. Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant. ENVIRONMENTAL MICROBIOME 2022; 17:3. [PMID: 35033203 PMCID: PMC8760730 DOI: 10.1186/s40793-022-00398-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Wastewater treatment plants are an essential part of maintaining the health and safety of the general public. However, they are also an anthropogenic source of antibiotic resistance genes. In this study, we characterized the resistome, the distribution of classes 1-3 integron-integrase genes (intI1, intI2, and intI3) as mobile genetic element biomarkers, and the bacterial and phage community compositions in the North End Sewage Treatment Plant in Winnipeg, Manitoba. Samples were collected from raw sewage, returned activated sludge, final effluent, and dewatered sludge. A total of 28 bacterial and viral metagenomes were sequenced over two seasons, fall and winter. Integron-integrase genes, the 16S rRNA gene, and the coliform beta-glucuronidase gene were also quantified during this time period. RESULTS Bacterial classes observed above 1% relative abundance in all treatments were Actinobacteria (39.24% ± 0.25%), Beta-proteobacteria (23.99% ± 0.16%), Gamma-proteobacteria (11.06% ± 0.09%), and Alpha-proteobacteria (9.18 ± 0.04%). Families within the Caudovirales order: Siphoviridae (48.69% ± 0.10%), Podoviridae (23.99% ± 0.07%), and Myoviridae (19.94% ± 0.09%) were the dominant phage observed throughout the NESTP. The most abundant bacterial genera (in terms of average percent relative abundance) in influent, returned activated sludge, final effluent, and sludge, respectively, includes Mycobacterium (37.4%, 18.3%, 46.1%, and 7.7%), Acidovorax (8.9%, 10.8%, 5.4%, and 1.3%), and Polaromonas (2.5%, 3.3%, 1.4%, and 0.4%). The most abundant class of antibiotic resistance in bacterial samples was tetracycline resistance (17.86% ± 0.03%) followed by peptide antibiotics (14.24% ± 0.03%), and macrolides (10.63% ± 0.02%). Similarly, the phage samples contained a higher prevalence of macrolide (30.12% ± 0.30%), peptide antibiotic (10.78% ± 0.13%), and tetracycline (8.69% ± 0.11%) resistance. In addition, intI1 was the most abundant integron-integrase gene throughout treatment (1.14 × 104 gene copies/mL) followed by intI3 (4.97 × 103 gene copies/mL) while intI2 abundance remained low (6.4 × 101 gene copies/mL). CONCLUSIONS Wastewater treatment successfully reduced the abundance of bacteria, DNA phage and antibiotic resistance genes although many antibiotic resistance genes remained in effluent and biosolids. The presence of integron-integrase genes throughout treatment and in effluent suggests that antibiotic resistance genes could be actively disseminating resistance between both environmental and pathogenic bacteria.
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Affiliation(s)
- Paul Jankowski
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Jaydon Gan
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Tri Le
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Michaela McKennitt
- Clayton H. Riddell Faculty of Environment, Earth, and Resources, University of Manitoba, Winnipeg, MB, Canada
- Institute of the Environment, University of Ottawa, Ottawa, ON, Canada
| | - Audrey Garcia
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Kadir Yanaç
- Department of Civil Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Qiuyan Yuan
- Department of Civil Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Miguel Uyaguari-Diaz
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada.
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26
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Iakovides IC, Manoli K, Karaolia P, Michael-Kordatou I, Manaia CM, Fatta-Kassinos D. Reduction of antibiotic resistance determinants in urban wastewater by ozone: Emphasis on the impact of wastewater matrix towards the inactivation kinetics, toxicity and bacterial regrowth. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126527. [PMID: 34329111 DOI: 10.1016/j.jhazmat.2021.126527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
This study investigated the impact of bench-scale ozonation on the inactivation of total cultivable and antibiotic-resistant bacteria (faecal coliforms, Escherichia coli, Pseudomonas aeruginosa, Enterococcus spp., and total heterotrophs), and the reduction of gene markers (16S rRNA and intl1) and antibiotic resistance genes (qacEΔ1, sul1, aadA1 and dfrA1) indigenously present in wastewater effluents treated by membrane bioreactor (MBR) or conventional activated sludge (CAS). The Chick-Watson model-predicted ozone exposure (CT) requirements, showed that higher CT values were needed for CAS- than MBR-treated effluents to achieve a 3-log reduction of each microbial group, i.e., ~30 and 10 gO3 min gDOC-1 respectively. Ozonation was efficient in inactivating the examined antibiotic-resistant bacteria, and no bacterial regrowth was observed after 72 h. The genes abundance decreased significantly by ozone, but an increase in their abundance was detected 72 h after storage of the treated samples. A very low removal of DOC was achieved and at the same time phyto- and eco-toxicity increased after the ozonation treatment in both wastewater matrices. The gene abundance, regrowth and toxicity results of this study may be of high environmental significance for comprehensive evaluation of ozone and may guide future studies in assessing these parameters for other oxidants/disinfectants.
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Affiliation(s)
- I C Iakovides
- Department of Civil and Environmental Engineering, School of Engineering, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus; Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - K Manoli
- Department of Civil and Environmental Engineering, School of Engineering, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus; Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - P Karaolia
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - I Michael-Kordatou
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - C M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua de Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - D Fatta-Kassinos
- Department of Civil and Environmental Engineering, School of Engineering, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus; Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus.
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27
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Yao S, Ye J, Yang Q, Hu Y, Zhang T, Jiang L, Munezero S, Lin K, Cui C. Occurrence and removal of antibiotics, antibiotic resistance genes, and bacterial communities in hospital wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:57321-57333. [PMID: 34089156 PMCID: PMC8177822 DOI: 10.1007/s11356-021-14735-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/01/2021] [Indexed: 05/05/2023]
Abstract
Hospital wastewater contains a variety of human antibiotics and pathogens, which makes the treatment of hospital wastewater essential. However, there is a lack of research on these pollutants at hospital wastewater treatment plants. In this study, the characteristics and removal of antibiotics and antibiotic resistance genes (ARGs) in the independent treatment processes of hospitals of different scales (primary hospital, H1; secondary hospital, H2; and tertiary hospital, H3) were investigated. The occurrence of antibiotics and ARGs in wastewater from three hospitals varied greatly. The first-generation cephalosporin cefradine was detected at a concentration of 2.38 μg/L in untreated wastewater from H1, while the fourth-generation cephalosporin cefepime had the highest concentration, 540.39 μg/L, at H3. Ofloxacin was detected at a frequency of 100% and had removal efficiencies of 44.2%, 51.5%, and 81.6% at H1, H2, and H3, respectively. The highest relative abundances of the β-lactam resistance gene blaGES-1 (1.77×10-3 copies/16S rRNA), the quinolone resistance gene qnrA (8.81×10-6 copies/16S rRNA), and the integron intI1 (1.86×10-4 copies/16S rRNA) were detected in the treated wastewater. The concentrations of several ARGs were increased in the treated wastewater (e.g. blaOXA-1, blaOXA-10, and blaTEM-1). Several pathogenic or opportunistic bacteria (e.g. Acinetobacter, Klebsiella, Aeromonas, and Pseudomonas) were observed at high relative abundances in the treated wastewater. These results suggested the co-occurrence of antibiotics, ARGs, and antibiotic-resistant pathogens in hospital wastewater, and these factors may spread into the receiving aquatic environment.
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Affiliation(s)
- Shijie Yao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jianfeng Ye
- Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Qing Yang
- Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Yaru Hu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Tianyang Zhang
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Lei Jiang
- National Engineering Research Center of Urban Water Resources, Shanghai, 200082, China
| | - Salvator Munezero
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Kuangfei Lin
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
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28
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Martin C, Stebbins B, Ajmani A, Comendul A, Hamner S, Hasan NA, Colwell R, Ford T. Nanopore-based metagenomics analysis reveals prevalence of mobile antibiotic and heavy metal resistome in wastewater. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1572-1585. [PMID: 33459951 DOI: 10.1007/s10646-020-02342-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
In-depth studies of the microbiome and mobile resistome profile of different environments is central to understanding the role of the environment in antimicrobial resistance (AMR), which is one of the urgent threats to global public health. In this study, we demonstrated the use of a rapid (and easily portable) sequencing approach coupled with user-friendly bioinformatics tools, the MinION (Oxford Nanopore Technologies), on the evaluation of the microbial as well as mobile metal and antibiotic resistome profile of semi-rural wastewater. A total of 20 unique phyla, 43 classes, 227 genera, and 469 species were identified in samples collected from the Amherst Wastewater Treatment Plant, both from primary and secondary treated wastewater. Alpha diversity indices indicated that primary samples were significantly richer and more microbially diverse than secondary samples. A total of 1041 ARGs, 68 MRGs, and 17 MGEs were detected in this study. There were more classes of AMR genes in primary than secondary wastewater, but in both cases multidrug, beta-lactam and peptide AMR predominated. Of note, OXA β-lactamases, some of which are also carbapenemases, were enriched in secondary samples. Metal resistance genes against arsenic, copper, zinc and molybdenum were the dominant MRGs in the majority of the samples. A larger proportion of resistome genes were located in chromosome-derived sequences except for mobilome genes, which were predominantly located in plasmid-derived sequences. Genetic elements related to transposase were the most common MGEs in all samples. Mobile or MGE/plasmid-associated resistome genes that confer resistance to last resort antimicrobials such as carbapenems and colistin were detected in most samples. Worryingly, several of these potentially transferable genes were found to be carried by clinically-relevant hosts including pathogenic bacterial species in the orders Aeromonadales, Clostridiales, Enterobacterales and Pseudomonadales. This study demonstrated that the MinION can be used as a metagenomics approach to evaluate the microbiome, resistome, and mobilome profile of primary and secondary wastewater.
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Affiliation(s)
| | | | - Asha Ajmani
- University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | | | | | - Nur A Hasan
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Rita Colwell
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Timothy Ford
- University of Massachusetts Lowell, Lowell, MA, 01854, USA.
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29
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Yang Y, Zhang AN, Che Y, Liu L, Deng Y, Zhang T. Underrepresented high diversity of class 1 integrons in the environment uncovered by PacBio sequencing using a new primer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 787:147611. [PMID: 34000537 DOI: 10.1016/j.scitotenv.2021.147611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Class 1 integrons (CL1s) are one of the major contributors to the horizontal transfer of antibiotic resistance genes (ARGs). However, our knowledge of CL1 in the environment is still very limited due to the limitations of the current PCR primers and the sequencing methods adopted. This study developed a new primer coupled with PacBio sequencing to investigate the underrepresented diversity of CL1s in a mixed environmental sample (i.e. activated sludge from wastewater treatment plant and pig feces from animal farm). The new primer successfully uncovered 20 extra ARGs subtypes and 57% (422/739) more unique integron array structures than the previous primers. Compared to the whole genome database, CL1s revealed in the environment in this study were of much greater diversity, having 93% (900/967) novel array structures. Antibiotic resistance is the predominant function (78.3% genes) carried by CL1, and a vast majority (98.6% genes) of them confer resistance to aminoglycoside, beta-lactam, trimethoprim, or chloramphenicol. Additionally, 78.5% unique CL1 arrays carried more than one ARGs, and 25.9% of them carried ARGs of clinical relevance with high transferability potential posing threat to the general public. Our results indicated the importance of CL1s in the spread of ARGs. Overall, combining PacBio sequencing with the new primer designed in this study largely broadened our knowledge of CL1s in the environment and their significance in the environmental proliferation of ARGs.
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Affiliation(s)
- Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong
| | - An-Ni Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong
| | - You Che
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong.
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30
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Buta M, Korzeniewska E, Harnisz M, Hubeny J, Zieliński W, Rolbiecki D, Bajkacz S, Felis E, Kokoszka K. Microbial and chemical pollutants on the manure-crops pathway in the perspective of "One Health" holistic approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 785:147411. [PMID: 33957582 DOI: 10.1016/j.scitotenv.2021.147411] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/15/2021] [Accepted: 04/24/2021] [Indexed: 05/23/2023]
Abstract
This study determined the impact of poultry and bovine manure fertilization on the content of antibiotics, heavy metals (HMs), and the quantitative and qualitative composition of integrase and antibiotic resistance genes in soil, groundwater, and crops cultivated on manure-amended plots. Antibiotic concentration levels were analyzed using the HPLC-MS/MS, heavy metal concentration level were measured by HGAAS and ICP-OES, while the integrase genes and ARGs were quantified using Real-Time PCR (qPCR) method. Manure, soil, and crops samples contained the highest concentration of Zn (104-105 ng gdm-1) and Cu (103-105 ng gdm-1) of all HMs tested. Manure-supplemented soil was characterised by a high concentration of doxycycline and enrofloxacin. A high abundance of integrase genes was noted in samples of manure (109-1010 copies gdm-1) and soil (107-108 copies gdm-1). Among all the analyzed genes, sul1, sul2, blaTEM, and integrase genes were the most common. Results of the study demonstrate the selective character of ARGs transfer from poultry and bovine manure to plants. The only gene to occur in all studied environmental compartments was sul1 (from 102 - groundwater to 1011 - poultry manure). It was also found that animal manure may cause an increase in the HMs concentration in soil and their accumulation in crops, which may influence the health of humans and animals consuming crops grown on manure-amended soil. The high abundance of integrase genes and ARGs and their reciprocal correlations with HMs pose a serious risk of the rapid spread of antibiotic resistance in the environment. Moreover, unusual dependencies between integrase genes and selected ARGs indicate the possibility of changes in the mobility nature of genetic elements.
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Affiliation(s)
- Martyna Buta
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland.
| | - Monika Harnisz
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland
| | - Jakub Hubeny
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland
| | - Wiktor Zieliński
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland
| | - Damian Rolbiecki
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland
| | - Sylwia Bajkacz
- The Biotechnology Centre, Silesian University of Technology, Krzywoustego 8 Str., 44-100 Gliwice, Poland; Department of Inorganic, Analytical Chemistry and Electrochemistry, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 6 Str., 44-100 Gliwice, Poland
| | - Ewa Felis
- The Biotechnology Centre, Silesian University of Technology, Krzywoustego 8 Str., 44-100 Gliwice, Poland; Environmental Biotechnology Department, Faculty of Energy and Environmental Engineering, Silesian University of Technology, Akademicka 2 Str., 44-100 Gliwice, Poland
| | - Klaudia Kokoszka
- The Biotechnology Centre, Silesian University of Technology, Krzywoustego 8 Str., 44-100 Gliwice, Poland; Department of Inorganic, Analytical Chemistry and Electrochemistry, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 6 Str., 44-100 Gliwice, Poland
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Li X, Wang P, Chu S, Su Y, Wu D, Xie B. The variation of antibiotic resistance genes and their links with microbial communities during full-scale food waste leachate biotreatment processes. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125744. [PMID: 33862482 DOI: 10.1016/j.jhazmat.2021.125744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/10/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
The prevalence of antibiotic resistance genes (ARGs) has been widely reported in various environments. However, little is known of them in food waste (FW) leachate with high organic content and how their distribution is influenced by biotreatment processes. Here, twelve ARGs, two integrase genes and bacterial communities were investigated during two full-scale FW biotreatment processes. High ARGs abundances (absolute: 1.03 × 107-2.82 × 109copies/mL; relative: 0.076-2.778copies/16S rRNA) were observed across all samples. Although biotreatment effectively reduced absolute abundance of ARGs, additional bacteria acquiring ARGs caused an increase in their relative abundance, which further increased the transmission risk of ARGs. mexF, blaCTX-M, sul1 played crucial roles and sul1 might be considered as an indicator for the prediction of total ARGs. It is worrying that the discharge (effluent and sludge) included highly abundant ARGs (5.09 × 1014-4.83 × 1015copies/d), integrons (1.11 × 1014-6.04 × 1014copies/d) and potential pathogens (such as Pseudomonas and Streptococcus), which should be given more attentions. blaCTX-M and tetQ possessed most potential hosts, Proteobacteria-L and Firmicutes-W were predominant contributors of ARGs-hosts at genus level. This study suggested FW leachate biotreatment systems could be reservoirs of ARGs and facilitated the proliferation of them. The exploration of effective removal methods and formulation of emission standard are necessary for future ARGs mitigation.
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Affiliation(s)
- Xunan Li
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Panliang Wang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Siqin Chu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Yinglong Su
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Engineering Research Center for Nanophotonics and Advanced Instrument, Ministry of Education, East China Normal University, Shanghai 200062, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Dong Wu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Engineering Research Center for Nanophotonics and Advanced Instrument, Ministry of Education, East China Normal University, Shanghai 200062, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Bing Xie
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Engineering Research Center for Nanophotonics and Advanced Instrument, Ministry of Education, East China Normal University, Shanghai 200062, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
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Pereira AR, Paranhos AGDO, de Aquino SF, Silva SDQ. Distribution of genetic elements associated with antibiotic resistance in treated and untreated animal husbandry waste and wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:26380-26403. [PMID: 33835340 DOI: 10.1007/s11356-021-13784-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Animal breeding for meat production based on swine, cattle, poultry, and aquaculture is an activity that generates several impacts on the environment, among them the spread of antibiotic resistance. There is a worldwide concern related to the massive use of antibiotics, which causes selective pressure on the microbial community, triggering bacteria that contain "antibiotic resistance genes." According to the survey here presented, antibiotic resistance-related genes such as tetracyclines (tet), erythromycin (erm), and sulfonamides (sul), as well as the genetic mobile element interferon (int), are the most reported genetic elements in qualitative and quantitative studies of swine, cattle, poultry, and aquaculture manure/wastewater. It has been observed that biological treatments based on waste composting and anaerobic digestion are effective in ARG removal, particularly for tet, bla, erm, and qnr (quinolone) genes. On the other hand, sul and intI genes were more persistent in such treatments. Tertiary treatments, such advanced oxidative processes, are suitable strategies to improve ARG reduction. In general temperature, hydraulic retention time, and penetration of sunlight are the main operational parameters for ARG reduction in treatments applied to animal waste, and therefore attention should be addressed to optimize their efficacy regarding ARG removal. Despite being reduced, the presence of ARG in treated effluents and in biosolids indicates that there is a potential risk of antibiotic resistance spread in nature, especially through the release of treated livestock waste into the environment.
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Affiliation(s)
- Andressa Rezende Pereira
- Graduate Program in Environmental Engineering, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, State of Minas Gerais, CEP: 35.400-000, Brazil
| | - Aline Gomes de Oliveira Paranhos
- Graduate Program in Environmental Engineering, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, State of Minas Gerais, CEP: 35.400-000, Brazil
| | - Sérgio Francisco de Aquino
- Department of Chemistry, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, State of Minas Gerais, CEP: 35.400-000, Brazil
| | - Silvana de Queiroz Silva
- Department of Biological Sciences, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, State of Minas Gerais, CEP: 35.400-000, Brazil.
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Zhang QQ, Ji XM, Tian GM, Jin RC. Evolution of microbial community and antibiotic resistance genes in anammox process stressed by oxytetracycline and copper. BIORESOURCE TECHNOLOGY 2021; 319:124106. [PMID: 32949830 DOI: 10.1016/j.biortech.2020.124106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
The individual and combined impacts of copper ion (Cu2+) and oxytetracycline (OTC) on anaerobic ammonium oxidation (anammox) performance and its self-recovery process were examined. Experimental results showed that the anammox performance and activity of anammox bacteria were inhibited by 1.0 mg L-1 OTC, Cu2+ and OTC + Cu2+, and both single and combined inhibitions were reversible. The abundance of functional genes and parts of antibiotic resistance genes (ARGs) were positively related to the dominant bacterium Ca. Kuenenia, implying that the recovery of the performance was associated with the progressive induction of potentially resistant species after inhibition. The above outcomes illustrated that anammox bacteria were stressed by metals and antibiotics, but they still could remove nitrogen at a rate higher than 20.6 ± 0.8 kg N m-3 d-1, providing guidance for engineering applications of anammox processes.
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Affiliation(s)
- Qian-Qian Zhang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; Department of Environmental Engineering, School of Water and Environment, Chang'an University, Xi'an 710061, China; Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Xiao-Ming Ji
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Guang-Ming Tian
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Ren-Cun Jin
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
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Dias MF, de Castro GM, de Paiva MC, de Paula Reis M, Facchin S, do Carmo AO, Alves MS, Suhadolnik ML, de Moraes Motta A, Henriques I, Kalapothakis E, Lobo FP, Nascimento AMA. Exploring antibiotic resistance in environmental integron-cassettes through intI-attC amplicons deep sequencing. Braz J Microbiol 2020; 52:363-372. [PMID: 33247398 DOI: 10.1007/s42770-020-00409-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/19/2020] [Indexed: 02/08/2023] Open
Abstract
INTRODUCTION Freshwater ecosystems provide propitious conditions for the acquisition and spread of antibiotic resistance genes (ARGs), and integrons play an important role in this process. MATERIAL AND METHODS In the present study, the diversity of putative environmental integron-cassettes, as well as their potential bacterial hosts in the Velhas River (Brazil), was explored through intI-attC and 16S rRNA amplicons deep sequencing. RESULTS AND DISCUSSION: ORFs related to different biological processes were observed, from DNA integration to oxidation-reduction. ARGs-cassettes were mainly associated with class 1 mobile integrons carried by pathogenic Gammaproteobacteria, and possibly sedentary chromosomal integrons hosted by Proteobacteria and Actinobacteria. Two putative novel ARG-cassettes homologs to fosB3 and novA were detected. Regarding 16SrRNA gene analysis, taxonomic and functional profiles unveiled Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as dominant phyla. Betaproteobacteria, Alphaproteobacteria, and Actinobacteria classes were the main contributors for KEGG orthologs associated with resistance. CONCLUSIONS Overall, these results provide new information about environmental integrons as a source of resistance determinants outside clinical settings and the bacterial community in the Velhas River.
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Affiliation(s)
- Marcela França Dias
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil.,Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Giovanni Marques de Castro
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | | | - Mariana de Paula Reis
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Susanne Facchin
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Anderson Oliveira do Carmo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Marta Salgueiro Alves
- Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal.,CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - Maria Luíza Suhadolnik
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Amanda de Moraes Motta
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Isabel Henriques
- CESAM, Universidade de Aveiro, Aveiro, Portugal.,Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, Coimbra, Portugal
| | - Evanguedes Kalapothakis
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Francisco Pereira Lobo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Andréa Maria Amaral Nascimento
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil.
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Niestępski S, Harnisz M, Korzeniewska E, Osińska A. Markers Specific to Bacteroides fragilis Group Bacteria as Indicators of Anthropogenic Pollution of Surface Waters. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17197137. [PMID: 33003501 PMCID: PMC7579016 DOI: 10.3390/ijerph17197137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 12/29/2022]
Abstract
The aim of this study was to evaluate the applicability of markers specific to Bacteroides fragilis group (BFG) bacteria as indicators of anthropogenic pollution of surface waters. In addition, the impact of wastewater treatment plants (WWTPs) on the spread of genes specific to fecal indicator bacteria and genes encoding antimicrobial resistance in water bodies was also determined. Samples of hospital wastewater (HWW), untreated wastewater (UWW), and treated wastewater (TWW) evacuated from a WWTP were collected, and samples of river water were taken upstream (URW) and downstream (DRW) from the wastewater discharge point to determine, by qPCR, the presence of genes specific to BFG, Escherichia coli and Enterococcus faecalis, and the abundance of 11 antibiotic resistance genes (ARGs) and two integrase genes. The total number of bacterial cells (TCN) in the examined samples was determined by fluorescence in situ hybridization (FISH). Genes specific to BFG predominated among the analyzed indicator microorganisms in HWW, and their copy numbers were similar to those of genes specific to E. coli and E. faecalis in the remaining samples. The abundance of genes specific to BFG was highly correlated with the abundance of genes characteristic of E. coli and E. faecalis, all analyzed ARGs and intI genes. The results of this study indicate that genes specific to BFG can be used in analyses of human fecal pollution, and as indicators of environmental contamination with ARGs. A significant increase in the copy numbers of genes specific to BFG, E. coli, and seven out of the 11 analyzed ARGs was noted in samples of river water collected downstream from the wastewater discharge point, which suggests that WWTPs are an important source of these genes in riparian environments.
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36
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Yang K, Chen QL, Chen ML, Li HZ, Liao H, Pu Q, Zhu YG, Cui L. Temporal Dynamics of Antibiotic Resistome in the Plastisphere during Microbial Colonization. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:11322-11332. [PMID: 32812755 DOI: 10.1021/acs.est.0c04292] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The increasing and simultaneous pollution of plastic debris and antibiotic resistance in aquatic environments makes plastisphere a great health concern. However, the development process of antibiotic resistome in the plastisphere is largely unknown, impeding risk assessment associated with plastics. Here, we profiled the temporal dynamics of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial composition in the plastisphere from initial microbial colonization to biofilm formation in urban water. A total of 82 ARGs, 12 MGEs, and 63 bacterial pathogens were detected in the plastisphere and categorized as the pioneering, intermediate, and persistent ones. The high number of five MGEs and six ARGs persistently detected in the whole microbial colonization process was regarded as a major concern because of their potential role in disseminating antibiotic resistance. In addition to genomic analysis, D2O-labeled single-cell Raman spectroscopy was employed to interrogate the ecophysiology of plastisphere in a culture-independent way and demonstrated that the plastisphere was inherently more tolerant to antibiotics than bacterioplankton. Finally, by combining persistent MGEs, intensified colonization of pathogenic bacteria, increased tolerance to antibiotic, and potential trophic transfer into a holistic risk analysis, the plastisphere was indicated to constitute a hot spot to acquire and spread antibiotic resistance and impose a long-term risk to ecosystems and human health. These findings provide important insights into the antibiotic resistome and ecological risk of the plastisphere and highlight the necessity for comprehensive surveillance of plastisphere.
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Affiliation(s)
- Kai Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Qing-Lin Chen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mo-Lian Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Hong-Zhe Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Hu Liao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Qiang Pu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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Niestępski S, Harnisz M, Ciesielski S, Korzeniewska E, Osińska A. Environmental fate of Bacteroidetes, with particular emphasis on Bacteroides fragilis group bacteria and their specific antibiotic resistance genes, in activated sludge wastewater treatment plants. JOURNAL OF HAZARDOUS MATERIALS 2020; 394:122544. [PMID: 32224375 DOI: 10.1016/j.jhazmat.2020.122544] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/13/2020] [Accepted: 03/14/2020] [Indexed: 06/10/2023]
Abstract
The aim of this study was to determine the effect of the activated sludge process on the abundance of anaerobic bacteria of the phylum Bacteroidetes, with special emphasis on Bacteroides fragilis group (BFG) bacteria, in twelve full-scale wastewater treatment plants. The composition of bacterial phyla and classes in wastewater samples were analyzed by next-generation sequencing. The presence of specific to BFG bacteria genes and the abundance of ARGs and genes encoding class 1 integrase in wastewater samples were determined by qPCR. Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were dominant bacterial phyla in wastewater samples. Next-generation sequencing revealed similar proportions of Bacteroidia (<1.0-8.2 % of all bacteria) in wastewater influents and effluents, which suggest that these microorganisms are not completely eliminated in the activated sludge process. The average copy numbers of specific to BFG bacteria gene, were 106, and 104 copies in 1 mL of wastewater influents and effluents, respectively. The results revealed a correlation between the abundance of BFG bacteria and BFG-specific genes encoding resistance to antibiotics. The observed changes in the prevalence of BFG-specific genes and ARGs in untreated and treated wastewater indicate that the activated sludge process decreases the number of gene copies in the effluent evacuated to the environment.
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Affiliation(s)
- Sebastian Niestępski
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland.
| | - Monika Harnisz
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland.
| | - Sławomir Ciesielski
- Department of Environmental Biotechnology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Słoneczna 45G, 10-719, Olsztyn, Poland.
| | - Ewa Korzeniewska
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland.
| | - Adriana Osińska
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland.
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Huyan J, Tian Z, Zhang Y, Zhang H, Shi Y, Gillings MR, Yang M. Dynamics of class 1 integrons in aerobic biofilm reactors spiked with antibiotics. ENVIRONMENT INTERNATIONAL 2020; 140:105816. [PMID: 32474215 DOI: 10.1016/j.envint.2020.105816] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/10/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Class 1 integrons are strongly associated with the dissemination of antibiotic resistance in bacteria. However, little is known about whether the presence of antibiotics affects the abundance of integrons and antibiotic resistance genes during biological wastewater treatment. To explore the roles of class 1 integrons in spreading antibiotic resistance genes in environmental compartments, the dynamics of integrons were followed in biofilm reactors treating synthetic wastewater respectively spiked with streptomycin (STM) and oxytetracycline (OTC). The relative abundance of the integron-integrase gene (intI1) increased 12 or 29-fold respectively when treated with STM or OTC, under incrementally increasing dosage regimes from 0 to 50 mg L-1. Significant increases in intI1 abundance initially occurred at an antibiotic dose of 0.1 mg L-1. At the beginning of the experiment, 51% to 64% of integrons carried no gene cassettes. In STM and OTC spiked systems, there was a significant increase in the proportion of integrons that contained resistance gene cassettes, particularly at intermediate and higher antibiotic concentrations. Gene cassettes encoding resistance to aminoglycosides, trimethoprim, beta-lactam, erythromycin, and quaternary ammonium compounds were all detected in the treated systems. Three tetracycline resistance genes (tetA, tetC, tetG) were significantly correlated with the abundance of intI1 (p < 0.01), despite no tet resistance being present as a gene cassette. Genome sequencing of isolates showed synteny between the tet resistance genes and intI1, mediated through linkage to transposable elements including Tn3, IS26 and ISCR3. Class 1 integrons appeared to be under positive selection in the presence of antibiotics, and might have actively acquired new gene cassettes during the experiment.
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Affiliation(s)
- Jiaoqi Huyan
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of the Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing 100049, China
| | - Zhe Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of the Chinese Academy of Sciences, 19A Yu-Quan Road, 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 the Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing 100049, China.
| | - Hong Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yanhong Shi
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of the Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing 100049, China.
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Zhao X, Shen JP, Zhang LM, Du S, Hu HW, He JZ. Arsenic and cadmium as predominant factors shaping the distribution patterns of antibiotic resistance genes in polluted paddy soils. JOURNAL OF HAZARDOUS MATERIALS 2020; 389:121838. [PMID: 31848095 DOI: 10.1016/j.jhazmat.2019.121838] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 11/29/2019] [Accepted: 12/05/2019] [Indexed: 05/28/2023]
Abstract
Heavy metals have been recognized as potential factors driving the evolution and development of antibiotic resistance. However, the relative effects of cadmium (Cd) and arsenic (As) on the prevalence and distribution of antibiotic resistance genes (ARGs) remain unclear. We investigated the co-selection effects of Cd and As on ARGs in 45 paddy soils polluted by heavy metals, using high-throughput quantitative PCR. A total of 119 ARGs and 9 mobile genetic elements (MGEs) were detected in all samples. Regression analysis showed that the single pollution index (PIAs and PICd) and Nemerow integrated pollution index (NIPI) both had significant and positive correlations with ARGs (P < 0.05), indicating the co-selective effects of Cd and As on ARGs distribution. The significant correlations between bacterial taxa and different ARGs in network analysis revealed potential hosts of ARGs. Structural equation models indicated that the effects of As on ARGs were stronger than that of Cd. The profile of ARGs could be impacted by Cd and As indirectly by strongly affecting the bacterial abundance. Overall, this study extended our knowledge about the co-selection of Cd and As on ARGs in paddy soil, and had important implications for assessing the potential risks of ARGs in paddy soils.
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Affiliation(s)
- Xiang Zhao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100085, China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100085, China.
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100085, China
| | - Shuai Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100085, China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville Victoria 3010, Australia
| | - Ji-Zheng He
- University of Chinese Academy of Sciences, Beijing, 100085, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville Victoria 3010, Australia
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Hastak P, Cummins ML, Gottlieb T, Cheong E, Merlino J, Myers GSA, Djordjevic SP, Roy Chowdhury P. Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital. Microb Genom 2020; 6:e000371. [PMID: 32374251 PMCID: PMC7371115 DOI: 10.1099/mgen.0.000371] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 04/03/2020] [Indexed: 11/29/2022] Open
Abstract
This study sought to assess the genetic variability of Escherichia coli isolated from bloodstream infections (BSIs) presenting at Concord Hospital, Sydney during 2013-2016. Whole-genome sequencing was used to characterize 81 E. coli isolates sourced from community-onset (CO) and hospital-onset (HO) BSIs. The cohort comprised 64 CO and 17 HO isolates, including 35 multidrug-resistant (MDR) isolates exhibiting phenotypic resistance to three or more antibiotic classes. Phylogenetic analysis identified two major ancestral clades. One was genetically diverse with 25 isolates distributed in 16 different sequence types (STs) representing phylogroups A, B1, B2, C and F, while the other comprised phylogroup B2 isolates in subclades representing the ST131, ST73 and ST95 lineages. Forty-seven isolates contained a class 1 integron, of which 14 carried blaCTX -M-gene. Isolates with a class 1 integron carried more antibiotic resistance genes than isolates without an integron and, in most instances, resistance genes were localized within complex resistance loci (CRL). Resistance to fluoroquinolones could be attributed to point mutations in chromosomal parC and gyrB genes and, in addition, two isolates carried a plasmid-associated qnrB4 gene. Co-resistance to fluoroquinolone and broad-spectrum beta-lactam antibiotics was associated with ST131 (HO and CO), ST38 (HO), ST393 (CO), ST2003 (CO) and ST8196 (CO and HO), a novel ST identified in this study. Notably, 10/81 (12.3 %) isolates with ST95 (5 isolates), ST131 (2 isolates), ST88 (2 isolates) and a ST540 likely carry IncFII-IncFIB plasmid replicons with a full spectrum of virulence genes consistent with the carriage of ColV-like plasmids. Our data indicate that IncF plasmids play an important role in shaping virulence and resistance gene carriage in BSI E. coli in Australia.
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Affiliation(s)
- Priyanka Hastak
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Max L. Cummins
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia
- Faculty of Medicine, University of Sydney, NSW Australia
| | - Elaine Cheong
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia
| | - John Merlino
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia
- Faculty of Medicine, University of Sydney, NSW Australia
| | - Garry S. A. Myers
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - Steven P. Djordjevic
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Piklu Roy Chowdhury
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
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Chen QL, Hu HW, Zhu D, Ding J, Yan ZZ, He JZ, Zhu YG. Host identity determines plant associated resistomes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113709. [PMID: 31838394 DOI: 10.1016/j.envpol.2019.113709] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/12/2019] [Accepted: 11/30/2019] [Indexed: 05/20/2023]
Abstract
Plant microbiome, as the second genome of plant, and the interface between human and environmental microbiome, represents a potential pathway of human exposure to environmental pathogens and resistomes. However, the impact of host identity on the profile of resistomes in plant phyllosphere is unclear and this knowledge is vital for establishing a framework to evaluate the dissemination of antibiotic resistance via the plant microbiome. Here, we explored the phyllosphere microbiome and resistomes in 12 selected plant species. By using High-throughput quantitative PCR, we identified a total of 172 unique resistance genes in plant phyllosphere microbiome, which was significantly divergent from the profile of resistomes in associated soils (Adonis, P < 0.01). Host identity had a significant effect on the plant resistome, which was mainly attributed to the dissimilarity of phyllosphere bacterial phylogeny across different plants. We identified a core set of plant resistomes shared in more than 80% of samples, which accounted for more than 64% of total resistance genes. These plant core resistomes conferred resistance to antibiotics that are commonly administered to humans and animals. Our findings extend our knowledge regarding the resistomes in plant phyllosphere microbiome and highlight the role of host identity in shaping the plant associated antibiotic resistance genes.
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Affiliation(s)
- Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jing Ding
- School of Environmental and Material Engineering, Yantai University, 30 Qingquan Road, Yantai, 264005, China
| | - Zhen-Zhen Yan
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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Fouz N, Pangesti KNA, Yasir M, Al-Malki AL, Azhar EI, Hill-Cawthorne GA, Abd El Ghany M. The Contribution of Wastewater to the Transmission of Antimicrobial Resistance in the Environment: Implications of Mass Gathering Settings. Trop Med Infect Dis 2020; 5:tropicalmed5010033. [PMID: 32106595 PMCID: PMC7157536 DOI: 10.3390/tropicalmed5010033] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/30/2020] [Accepted: 02/15/2020] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial resistance (AMR) is the major issue posing a serious global health threat. Low- and middle-income countries are likely to be the most affected, both in terms of impact on public health and economic burden. Recent studies highlighted the role of resistance networks on the transmission of AMR organisms, with this network being driven by complex interactions between clinical (e.g., human health, animal husbandry and veterinary medicine) and other components, including environmental factors (e.g., persistence of AMR in wastewater). Many studies have highlighted the role of wastewater as a significant environmental reservoir of AMR as it represents an ideal environment for AMR bacteria (ARB) and antimicrobial resistant genes (ARGs) to persist. Although the treatment process can help in removing or reducing the ARB load, it has limited impact on ARGs. ARGs are not degradable; therefore, they can be spread among microbial communities in the environment through horizontal gene transfer, which is the main resistance mechanism in most Gram-negative bacteria. Here we analysed the recent literature to highlight the contribution of wastewater to the emergence, persistence and transmission of AMR under different settings, particularly those associated with mass gathering events (e.g., Hajj and Kumbh Mela).
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Affiliation(s)
- Nour Fouz
- The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia;
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Krisna N. A. Pangesti
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (K.N.A.P.); (G.A.H.-C.)
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.Y.); (E.I.A.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Abdulrahman L. Al-Malki
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Esam I. Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.Y.); (E.I.A.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Grant A. Hill-Cawthorne
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (K.N.A.P.); (G.A.H.-C.)
| | - Moataz Abd El Ghany
- The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia;
- The Marie Bashir Institute of Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW 2145, Australia
- The Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2145, Australia
- Correspondence: or
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Zheng W, Huyan J, Tian Z, Zhang Y, Wen X. Clinical class 1 integron-integrase gene - A promising indicator to monitor the abundance and elimination of antibiotic resistance genes in an urban wastewater treatment plant. ENVIRONMENT INTERNATIONAL 2020; 135:105372. [PMID: 31838265 DOI: 10.1016/j.envint.2019.105372] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/31/2019] [Accepted: 11/27/2019] [Indexed: 06/10/2023]
Abstract
In this study, 295 antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) from the influent, activated sludge (AS), and membrane bioreactor (MBR) permeate were primarily examined in the wastewater treatment plant (WWTP) biweekly over 13 months. The absolute concentrations of ARGs and MGEs respectively ranged from 1.27 × 1010 to 1.94 × 1011 and 8.00 × 109 to 1.24 × 1011 copies/L in the influent, of which were reduced by 2 to 3 orders of magnitude in the permeate. No significant seasonal variation of ARGs and MGEs was found in the WWTP, except that the absolute abundance of ARGs and MGEs in the AS was peaked during spring. The antibiotics affected neither ARGs nor MGEs significantly, suggesting their concentrations may be not high enough to pose a selective pressure. In contrast, the bacterial community had direct effect on the MGEs variation, meanwhile the MGEs influenced the ARG abundance directly. Class 1 integron-integrase gene (intI1), clinical intI1, and Tn21 associated more frequently with ARGs in the AS over long-term, suggesting the potential of them involved in horizontal gene transfer. Both intI1 and clinical intI1 had significantly positive associations with the overall abundance of ARGs, as well as significantly negative relationships with the overall removal rates of ARGs in the MBR. However, the abundances between intI1 and clinical intI1 were significantly different. Meanwhile, clinical intI1 remained rather consistent proportion with the ARG abundance in the AS and permeate, was stronger correlated with human pathogens, and was associated with greater number of ARGs over time. Moreover, clinical intI1 was significantly associated with the removal efficiency of ARGs from all classes. Taken together, clinical intI1 can be adopted as an indicator for the abundance and removal efficiency of ARGs in the WWTP.
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Affiliation(s)
- Wanlin Zheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Beijing Enterprises Water Group (China) Investment Limited, Beijing 100102, China
| | - Jiaoqi Huyan
- 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
| | - Zhe Tian
- 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.
| | - Xianghua Wen
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Yan ZZ, Chen QL, Zhang YJ, He JZ, Hu HW. Antibiotic resistance in urban green spaces mirrors the pattern of industrial distribution. ENVIRONMENT INTERNATIONAL 2019; 132:105106. [PMID: 31473416 DOI: 10.1016/j.envint.2019.105106] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/05/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
Urban green spaces are closely related to the activities and health of urban residents. Turf grass and soil are two major interfaces between the environmental and human microbiome, which represent potential pathways for the spread of antibiotic resistance genes (ARGs) from environmental to human microbiome through skin-surface contact. However, the information regarding the prevalence of ARGs in urban green spaces and drivers in shaping their distribution patterns remain unclear. Here, we profiled a wide spectrum of ARGs in grass phyllosphere and soils from 40 urban parks across Greater Melbourne, Australia, using high throughput quantitative PCR. A total of 217 and 218 unique ARGs and MGEs were detected in grass phyllosphere and soils, respectively, conferring resistance to almost all major classes of antibiotics commonly used in human and animals. The plant microbiome contained a core resistome, which occupied >84% of the total abundance of ARGs. In contrast, no core resistome was identified in the soil microbiome. The difference between plant and soil resistome composition was attributed to the difference in bacterial community structure and intensity of environmental and anthropogenic influence. Most importantly, the abundance of ARGs in urban green spaces was significantly positively related to industrial factors including total number of business, number of manufacturing, and number of electricity, gas, water and waste services in the region. Structural equation models further revealed that industrial distribution was a major factor shaping the ARG profiles in urban green spaces after accounting for multiple drivers. These findings have important implications for mitigation of the potential risks posed by ARGs to urban residents.
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Affiliation(s)
- Zhen-Zhen Yan
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, VIC 3010, Australia
| | - Qing-Lin Chen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, VIC 3010, Australia.
| | - Yu-Jing Zhang
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, VIC 3010, Australia
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, VIC 3010, Australia
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, VIC 3010, Australia.
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Ding J, Yin Y, Sun AQ, Lassen SB, Li G, Zhu D, Ke X. Effects of biochar amendments on antibiotic resistome of the soil and collembolan gut. JOURNAL OF HAZARDOUS MATERIALS 2019; 377:186-194. [PMID: 31163347 DOI: 10.1016/j.jhazmat.2019.05.089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/26/2019] [Accepted: 05/27/2019] [Indexed: 06/09/2023]
Abstract
A diverse array of ARGs has been detected in the guts of soil fauna residing in farmland soil. Biochar has been widely used in farmland for soil remediation and improvement of soil quality; however, the effects of biochar amendment on the gut-associated ARGs of soil fauna remain unclear. In the present study, collembolans were cultivated in soils amended with 6 types of biochars. High-throughput qPCR was used to establish ARG profiles of the collembolan guts as well as the surrounding soils. A total of 73 and 162 subtypes of ARGs were detected in the collembolan guts and soils, respectively. Biochar amendment significantly altered the ARG compositions of the collembolan guts and soils, in a biochar quality-dependent manner. However, only manure-derived biochar, which contained elevated concentrations of heavy metals, increased the relative abundance of gut-associated ARGs. Changes in the gut microbial community, MGEs and biochar properties explained 84% of the total ARG variations in the collembolan guts. The findings of this study suggested that biochar properties should receive more attention, as high doses of heavy metals in biochar could increase the abundance of ARGs in collembolan guts, thereby contributing to the spread of ARGs in the environment through collembolan movement.
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Affiliation(s)
- Jing Ding
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China
| | - Yue Yin
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - An-Qi Sun
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Simon Bo Lassen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
| | - Xin Ke
- Institute of Plant Physiology and Ecology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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Lu T, Zhu Y, Ke M, Peijnenburg WJGM, Zhang M, Wang T, Chen J, Qian H. Evaluation of the taxonomic and functional variation of freshwater plankton communities induced by trace amounts of the antibiotic ciprofloxacin. ENVIRONMENT INTERNATIONAL 2019; 126:268-278. [PMID: 30825745 DOI: 10.1016/j.envint.2019.02.050] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Ciprofloxacin (CIP), one of the most frequently detected antibiotics in water systems, has become an aquatic contaminant because of improper disposal and excretion by humans and animals. It is still unknown how trace amounts of CIP affect the aquatic microbial community diversity and function. We therefore investigated the effects of CIP on the structure and function of freshwater microbial communities via 16S/18S rRNA gene sequencing and metatranscriptomic analyses. CIP treatment (7 μg/L) did not significantly alter the physical and chemical condition of the water body as well as the composition of the main species in the community, but slightly increased the relative abundance of cyanobacteria and decreased the relative abundance of eukaryotes. Metatranscriptomic results showed that bacteria enhanced their phosphorus transport and photosynthesis after CIP exposure. The replication, transcription, translation and cell proliferation were all suppressed in eukaryotes, while the bacteria were not affected in any of these aspects. This interesting phenomenon was the exact opposite to both the antibacterial property of CIP and its safety for eukaryotes. We hypothesize that reciprocal and antagonistic interactions in the microcosm both contribute to this result: cyanobacteria may enhance their tolerance to CIP through benefiting from cross-feeding and some secreted substances that withstand bacterial CIP stress would also affect eukaryotic growth. The present study thus indicates that a detailed assessment of the aquatic ecotoxicity of CIP is essential, as the effects of CIP are much more complicated in microbial communities than in monocultures. CIP will continue to be an environmental contaminant due to its wide usage and production and more attention should be given to the negative effects of antibiotics as well as other bioactive pollutants on aquatic environments.
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Affiliation(s)
- Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Youchao Zhu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, RA, Leiden 2300, the Netherlands; National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, P.O. Box 1, Bilthoven, the Netherlands
| | - Meng Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tingzhang Wang
- Key laboratory of microbial technology and bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Jun Chen
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310021, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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Zhao Y, Cocerva T, Cox S, Tardif S, Su JQ, Zhu YG, Brandt KK. Evidence for co-selection of antibiotic resistance genes and mobile genetic elements in metal polluted urban soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 656:512-520. [PMID: 30529954 DOI: 10.1016/j.scitotenv.2018.11.372] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/19/2018] [Accepted: 11/24/2018] [Indexed: 05/20/2023]
Abstract
Antibiotic resistance genes (ARGs) constitute emerging environmental pollutants and pose risks to public health. Toxic metals are known to select for metal-resistant bacteria in metal-contaminated soils, but there is growing concern that metal contaminants can also act as co-selective agents thereby causing environmental proliferation of antibiotic resistance. In this study, we quantified ARGs and selected mobile genetic elements (MGEs) known to constitute potential ARG hosts in 50 archived urban and suburban soils from the Belfast metropolitan area using a high-throughput qPCR ARG chip. ARG prevalence was linked to concentrations of individual metals and a soil metal toxicity index calculated based on the relative toxicity of different metals to soil microbial processes. A total of 164 ARGs were detected across the 50 soils analyzed with an average absolute abundance of 3.4 × 107 ARG gene copies per gram of soil. A significant correlation between abundance of ARGs and MGEs was observed, suggesting the importance of horizontal gene transfer for ARG dissemination. Network analysis revealed significant co-occurrence patterns between specific metals (As, Cd, Co, Cr, Cu. Hg, Ni and Zn) and associated ARGs. Path analysis further indicated that the soil metal toxicity index significantly affected the number of detected ARGs (λ = 0.32, P < 0.001) and the abundance of metal co-occurring ARGs (λ = 0.612, P < 0.001) via effects on MGEs. Collectively, our results indicate a role of soil metals in co-selection of ARGs and MGEs in urban and semi-urban soils and suggest a risk for environmental ARG dissemination via horizontal gene transfer.
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Affiliation(s)
- Yi Zhao
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark.
| | - Tatiana Cocerva
- School of Natural and Built Environment, Queen's University of Belfast, David Keir Building, Stranmillis Road, Belfast BT9 6AX, United Kingdom
| | - Siobhan Cox
- School of Natural and Built Environment, Queen's University of Belfast, David Keir Building, Stranmillis Road, Belfast BT9 6AX, United Kingdom
| | - Stacie Tardif
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Kristian Koefoed Brandt
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark; Sino-Danish Centre for Education and Research, Huairou District, Beijing, China.
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Ding J, Zhu D, Hong B, Wang HT, Li G, Ma YB, Tang YT, Chen QL. Long-term application of organic fertilization causes the accumulation of antibiotic resistome in earthworm gut microbiota. ENVIRONMENT INTERNATIONAL 2019; 124:145-152. [PMID: 30641258 DOI: 10.1016/j.envint.2019.01.017] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 05/11/2023]
Abstract
Antibiotic resistance genes (ARGs), prevalent across multiple environmental media, threaten human health worldwide and are considered emerging environmental contaminants. Earthworm gut, a niche for bacteria to survive, represents a potential reservoir for ARGs in soil. However, the compositions of ARGs in the earthworm gut microbiota remain elusive, especially under field conditions. In this study, we applied high-throughput quantitative PCR to profile the ARGs in the gut microbiota of earthworms after chronic exposure to fertilizers. To elucidate the factors that impact the ARGs composition, the bacterial community of gut microbiota, mobile genetic elements (MGEs), soil (nutrients, heavy metals, and antibiotics) and the properties of gut content (pH and nutrients) were analyzed. A total of 98 subtypes among 9 major types of ARGs, and 3 different MGEs were detected in the gut microbiota of earthworms. Organic fertilizer (sewage sludge and chicken manure) application significantly increased the diversity and abundance of ARGs. Of the 1123 identified operational taxonomic units (OTUs) at 97% similarity cutoff, most of them were assigned to Firmicutes (55.5%) and Proteobacteria (33.6%) in earthworm gut microbiota. Long-term organic fertilization slightly changed the microbiota composition, but did not impact the diversity. Partial redundancy analysis (pRDA) revealed that bacterial community, combined with environmental factors (soil and gut content properties) and MGEs, explained 72% of the variations of ARGs in the earthworm gut. Furthermore, the co-occurrence pattern between ARGs and MGEs indicated that horizontal gene transfer via MGEs may occur in the earthworm gut. These findings improve the current understanding of the dynamics of soil fauna-associated ARGs and the gut microbiota of earthworms may be an underappreciated hotspot for ARGs in the environment.
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Affiliation(s)
- Jing Ding
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Hong
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hong Tao Wang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yi Bing Ma
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Nutrient Cycling, Institute of Agriculture Resources and Regional Planning, Chinese Academy of Agriculture Sciences, Beijing 100081, China
| | - Yu Ting Tang
- School of Geographical Sciences, University of Nottingham, Ningbo 315100, China
| | - Qing Lin Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Prevalence of Antibiotic Resistance Genes in Air-Conditioning Systems in Hospitals, Farms, and Residences. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16050683. [PMID: 30813565 PMCID: PMC6427721 DOI: 10.3390/ijerph16050683] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/19/2019] [Accepted: 02/22/2019] [Indexed: 01/08/2023]
Abstract
High-throughput quantitative PCR combined with Illumina sequencing and network analysis were used to characterize the antibiotic resistance gene (ARG) profiles in air-conditioning filters from different environments. In total, 177 ARGs comprising 10 ARG types were determined. The detectable numbers and the relative abundance of ARGs in hospitals and farms were significantly higher than those in city and village residences. Compared to hospitals, farms had a higher level of tetracycline, multidrug, integrase, and macrolide⁻lincosamide⁻streptogramin (MLS) B resistance genes but a lower level of beta-lactam resistance genes. The bl3_cpha gene was the most abundant resistance gene subtype in hospital samples with an abundance of 2.01 × 10-4 copies/16S rRNA, while a level of only 5.08 × 10-12 copies/16S rRNA was observed in farm samples. There was no significant difference in bacterial diversity among the hospitals, farms, and residences, and Proteobacteria was the most abundant phylum. Network analysis revealed that Proteobacteria and Actinobacteria were possible hosts of the beta-lactam, MLSB, aminoglycoside, multidrug, sulfonamide, and tetracycline resistance genes. The results demonstrate that ARGs exist in indoor environments and that farms and hospitals are important sources. This study provides a useful reference for understanding the distribution patterns and risk management of ARGs in indoor environments.
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Tong J, Lu X, Zhang J, Angelidaki I, Wei Y. Factors influencing the fate of antibiotic resistance genes during thermochemical pretreatment and anaerobic digestion of pharmaceutical waste sludge. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:1403-1413. [PMID: 30278414 DOI: 10.1016/j.envpol.2018.09.096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 05/16/2023]
Abstract
The prevalence of antibiotic resistance genes (ARGs) in waste sludge, especially for the pharmaceutical waste sludge, presents great potential risks to human health. Although ARGs and factors affecting their spreading are of major importance for human health, the factors influencing the fate of ARGs during sludge treatment, especially for pharmaceutical sludge treatment are not yet well understood. In order to be able to minimize ARGs spreading, it is important to find what is influencing their spreading. Therefore, certain factors, such as the sludge characteristics, bacterial diversity and community composition, and mobile genetic elements (MGEs) during the advanced AD of pharmaceutical sludge with different pretreatments were studied, and their affinity with ARGs was elucidated by Spearman correlation analysis. Furthermore, multiple linear regression was introduced to evaluate the importance of the various factors. Results showed that 59.7%-88.3% of the variations in individual ARGs and total ARGs can be explained by the corresponding factors. Bacterial diversity rather than specific bacterial community composition affected the fate of ARGs, whereas alkalinity was the most important factor on ARGs among all sludge characteristics investigated in this study. Besides, 66.4% of variation of total ARGs was driven by the changes of MGEs. Multiple linear regression models also reveal the collective effect of these factors on ARGs, and the contributions of each factor impact on ARGs. This study provides more comprehension about the factors impact on the fate of ARGs during pharmaceutical sludge treatment, and offers an approach to evaluate the importance of each factor, which method could be introduced for evaluation of factors influencing ARGs during other types of sludge or wastewater treatment.
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Affiliation(s)
- Juan Tong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xueting Lu
- Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Copenhagen Lyngby, 2800, Denmark
| | - Yuansong Wei
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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