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Bosch J, Bezuidenhout C, Coertze R, Molale-Tom L. Metal- and antibiotic-resistant heterotrophic plate count bacteria from a gold mine impacted river: the Mooi River system, South Africa. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:31605-31619. [PMID: 36449242 PMCID: PMC9995416 DOI: 10.1007/s11356-022-24015-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/01/2022] [Indexed: 04/16/2023]
Abstract
The Wonderfonteinspruit, South Africa, is highly impacted by a century of gold mining activities. The aim of this study was to investigate the physico-chemical properties of the Wonderfonteinspruit and the receiving Mooi River system, the levels of antimicrobial (metals and antibiotics) resistance characteristics and heterotrophic bacteria levels in these water systems. Various physico-chemical parameters were determined. R2A agar and R2A agar supplemented with antimicrobials were used to enumerate heterotrophic bacteria. Morphologically distinct antimicrobial-resistant isolates were purified and screened for antibiotic susceptibility by a disc diffusion method. Selected isolates were identified, and minimum inhibitory concentration ranges determined. Among the antimicrobial resistant isolates, 87% were resistant to at least one antibiotic. Of these, almost 50% were resistant to more than 3 antibiotic classes. A large proportion was resistant to all 7 antibiotics tested. Phyla detected were Proteobacteria, Firmicutes and Bacteriodetes. High MIC levels for metals and antibiotics were detected among all the genera. Results demonstrate potential impacts of physico-chemical properties on levels of antimicrobial-resistant bacteria. Metal-resistant bacteria were also resistant to multiple antibiotics, suggesting that metal pollution from mining may be responsible for co-selection and maintenance of antibiotic-resistant bacteria in this aquatic system.
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Affiliation(s)
- Janita Bosch
- Unit for Environmental Sciences and Management, Microbiology, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - Carlos Bezuidenhout
- Unit for Environmental Sciences and Management, Microbiology, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - Roelof Coertze
- Unit for Environmental Sciences and Management, Microbiology, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - Lesego Molale-Tom
- Unit for Environmental Sciences and Management, Microbiology, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom, 2520, South Africa.
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Murray AK, Zhang L, Snape J, Gaze WH. Functional metagenomic libraries generated from anthropogenically impacted environments reveal importance of metabolic genes in biocide and antibiotic resistance. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 4:100184. [PMID: 36908773 PMCID: PMC9995290 DOI: 10.1016/j.crmicr.2023.100184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
Abstract
Anthropogenic activities result in the release of antimicrobial resistant bacteria and a cocktail of antimicrobial compounds into the environment that may directly select or indirectly co-select for antimicrobial resistance (AMR). Many studies use metagenome sequencing or qPCR-based approaches to study the environmental resistome but these methods are limited by a priori knowledge. In this study, a functional metagenomic approach was used to explore biocide resistance mechanisms in two contaminated environments and a pristine site, and to identify whether potentially novel genes conferring biocide resistance also conferred resistance or reduced susceptibility to antibiotics. Resistance was predominately mediated through novel mechanisms exclusive of the well-known qac efflux genes. UDP-galactose 4-epimerase (galE) -like genes were identified in both contaminated environments and were shown to confer cross-resistance to biocides and clinically important antibiotics for the first time (to our knowledge), compared to knockout mutants. GalE -like genes were also co-located with transposons, suggesting mobilisation potential. These results show that housekeeping genes may play a significant yet underappreciated role in AMR in environmental microbiomes.
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Affiliation(s)
- Aimee K. Murray
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, Cornwall TR10 9FE, United Kingdom
- Corresponding author.
| | - Lihong Zhang
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Jason Snape
- AstraZeneca Global Environment, Alderly Park, Macclesfield, United Kingdom
| | - William H. Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, Cornwall TR10 9FE, United Kingdom
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Yao Y, Liu Z, Yip KK, Pu Y, Cheng W, Li M, Habimana O. Cross-regional scale pollution of freshwater biofilms unveiled by antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151835. [PMID: 34822887 DOI: 10.1016/j.scitotenv.2021.151835] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
A comprehensive global profile of the distribution of ARGs in freshwater biofilms is lacking. We utilized metagenomic approaches to reveal the diversity, abundance, transferability and hosts of ARGs in 96 freshwater biofilm samples from 38 sampling sites across four countries. The abundant ARGs were associated with bacitracin, multidrug, polymyxin macrolide-lincosamide-streptogramin (MLS) aminoglycoside, β-lactam, chloramphenicol, sulfonamide and tetracycline resistance, consistent with the spectrum of antibiotics commonly used in human or veterinary medicine. As expected, the resistome in freshwater biofilm habitats was significantly influenced by geographical location and human footprint. Based on the co-occurrence pattern revealed by network analysis, mdtC, kdpE, and emrB were proposed as ARG indicators in freshwater biofilms that can be used to evaluate the abundance of 46 other co-occurring ARG subtypes quantitatively. Metagenomic assembly analysis revealed that the identified ARGs were hosted by more than 46 bacterial phyla, including various pathogens, which greatly expands the knowledge of resistome diversity in freshwater biofilms. Our study points to the central roles of biofilms in harbouring ARGs. The results could enhance understanding the distribution of ARGs in freshwater habitats, thereby strengthening the global environmental risk assessment and management of ARGs.
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Affiliation(s)
- Yuan Yao
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Zongbao Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Ka Kin Yip
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Yang Pu
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Wenda Cheng
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
| | - Olivier Habimana
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; The University Hong Kong Shenzhen Institute of Research and Innovation (HKU-SIRI), Shenzhen, Guangdong Province, China.
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A Comparative Analysis of Aquatic and Polyethylene-Associated Antibiotic-Resistant Microbiota in the Mediterranean Sea. BIOLOGY 2021; 10:biology10030200. [PMID: 33800749 PMCID: PMC8001005 DOI: 10.3390/biology10030200] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 12/15/2022]
Abstract
In this study, we evaluated the microbiome and the resistome profile of water and fragments of polyethylene (PE) waste collected at the same time from a stream and the seawater in a coastal area of Northwestern Sicily. Although a core microbiome was determined by sequencing of the V3-V4 region of the bacterial 16S rDNA gene, quantitative differences were found among the microbial communities on PE waste and the corresponding water samples. Our findings indicated that PE waste contains a more abundant and increased core microbiome diversity than the corresponding water samples. Moreover, PCR analysis of specific antibiotic resistance genes (ARGs) showed that PE waste harbors more ARGs than the water samples. Thus, PE waste could act as a carrier of antibiotic-resistant microbiota, representing an increased danger for the marine environment and living organisms, as well.
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The Household Resistome: Frequency of β-Lactamases, Class 1 Integrons, and Antibiotic-Resistant Bacteria in the Domestic Environment and Their Reduction during Automated Dishwashing and Laundering. Appl Environ Microbiol 2020; 86:AEM.02062-20. [PMID: 32978137 PMCID: PMC7657631 DOI: 10.1128/aem.02062-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/20/2020] [Indexed: 11/20/2022] Open
Abstract
Households provide a habitat for bacteria originating from humans, animals, foods, contaminated clothes, or other sources. Thus, bacteria carrying antibiotic resistance genes (ARGs) may be introduced via household members, animals, or the water supply from external habitats into private households and vice versa. Since data on antibiotic resistance (ABR) in the domestic environment are limited, this study aimed to determine the abundance of β-lactamase, mobile colistin resistance, and class 1 integron genes and the correlation of their presence and to characterize phenotypically resistant strains in 54 private households in Germany. Additionally, the persistence of antibiotic-resistant bacteria during automated dishwashing compared to that during laundering was assessed. Shower drains, washing machines, and dishwashers were sampled and analyzed using quantitative real-time PCR. Resistant strains were isolated, followed by identification and antibiotic susceptibility testing using a Vitek 2 system. The results showed a significantly higher relative ARG abundance of 0.2367 ARG copies/16S rRNA gene copies in shower drains than in dishwashers (0.1329 ARG copies/16S rRNA gene copies) and washing machines (0.0006 ARG copies/16S rRNA gene copies). bla CMY-2, bla ACT/MIR, and bla OXA-48 were the most prevalent ARG, and intI1 occurred in 96.3% of the households, while no mcr genes were detected. Several β-lactamase genes co-occurred, and the resistance of bacterial isolates correlated positively with genotypic resistance, with carbapenemase genes dominating across isolates. Antibiotic-resistant bacteria were significantly reduced during automated dishwashing as well as laundering tests and did not differ from susceptible strains. Overall, the domestic environment may represent a potential reservoir of β-lactamase genes and β-lactam-resistant bacteria, with shower drains being the dominant source of ABR.IMPORTANCE The abundance of antibiotic-resistant bacteria and ARGs is steadily increasing and has been comprehensively analyzed in natural environments, animals, foods, and wastewater treatment plants. In this respect, β-lactams and colistin are of particular interest due to the emergence of multidrug-resistant Gram-negative bacteria. Despite the connection of private households to these environments, only a few studies have focused on the domestic environment so far. Therefore, the present study further investigated the occurrence of ARGs and antibiotic-resistant bacteria in shower drains, washing machines, and dishwashers. The analysis of the domestic environment as a potential reservoir of resistant bacteria is crucial to determine whether households contribute to the spread of ABR or may be a habitat where resistant bacteria from the natural environment, humans, food, or water are selected due to the use of detergents, antimicrobial products, and antibiotics. Furthermore, ABR could limit the options for the treatment of infections arising in the domestic environment.
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Chen YR, Guo XP, Niu ZS, Lu DP, Sun XL, Zhao S, Hou LJ, Liu M, Yang Y. Antibiotic resistance genes (ARGs) and their associated environmental factors in the Yangtze Estuary, China: From inlet to outlet. MARINE POLLUTION BULLETIN 2020; 158:111360. [PMID: 32573452 DOI: 10.1016/j.marpolbul.2020.111360] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
The occurrence of antibiotic resistance genes (ARGs) and their associated environmental factors in estuaries are poorly understood. In this study, we comprehensively analyzed ARGs in both water and sediments from inlet to outlet of the Yangtze Estuary, China. The relative abundances of ARGs were higher in the turbidity maximum zone (TMZ) than other sites, implying that suspended particulate matter (SPM) was the major reservoir for ARGs in water. ARGs showed an increasing trend from inlet to outlet in sediments. Positively correlation between intI1 and sul1 in both water and sediments indicated that sul1 may be regulated by intI1. Correlation analysis and redundancy analysis showed that the spatial variations of estuarine ARGs were positively correlated with sample properties (e.g., temperature, SPM, pH) and chemical pollutants (e.g., heavy metals and antibiotic residues), among which chemical pollutants were the major drivers for the ARG distribution in both water and sediments.
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Affiliation(s)
- Yu-Ru Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xing-Pan Guo
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zuo-Shun Niu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Da-Pei Lu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiao-Li Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Sai Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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Almakki A, Jumas-Bilak E, Marchandin H, Licznar-Fajardo P. Antibiotic resistance in urban runoff. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 667:64-76. [PMID: 30826682 DOI: 10.1016/j.scitotenv.2019.02.183] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 05/24/2023]
Abstract
Aquatic ecosystems subjected to anthropogenic pressures are places of rapid evolution of microbial communities and likely hotspots for selection and emergence of antibiotic resistant bacteria. In urban settings, water quality and the risk of infection are generally assessed in sewers and in effluents of wastewater treatment plants. Physical and chemical parameters as well as the presence of antibiotics, antibiotic-resistant bacteria and genes of resistance are driven by urban activities, with adverse effects on aquatic ecosystems. In this paper we review the environmental pressures exerted on bacterial communities in urban runoff waters and discuss the impact of these settings on antibiotic resistance. Considering the worrisome epidemiology of infectious diseases and estimated mortality due to antimicrobial resistance in the coming decades, there is an urgent need to identify all environmental reservoirs of resistant bacteria and resistance genes to complete our knowledge of the epidemiological cycle and of the dynamics of urban antibiotic resistance.
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Affiliation(s)
- Ayad Almakki
- HSM, Univ Montpellier, IRD, CNRS, Montpellier, France; Department of Clinical Laboratory Science, College of Pharmacy, University of Basrah, Iraq
| | - Estelle Jumas-Bilak
- HSM, Univ Montpellier, IRD, CNRS, Département d'Hygiène Hospitalière, CHU de Montpellier, Montpellier, France
| | - Hélène Marchandin
- HSM, Univ Montpellier, IRD, CNRS, Montpellier, France, Département de Microbiologie, CHU Nîmes, Nîmes, France
| | - Patricia Licznar-Fajardo
- HSM, Univ Montpellier, IRD, CNRS, Département d'Hygiène Hospitalière, CHU de Montpellier, Montpellier, France.
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Liu X, Zhang G, Liu Y, Lu S, Qin P, Guo X, Bi B, Wang L, Xi B, Wu F, Wang W, Zhang T. Occurrence and fate of antibiotics and antibiotic resistance genes in typical urban water of Beijing, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 246:163-173. [PMID: 30543942 DOI: 10.1016/j.envpol.2018.12.005] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 12/01/2018] [Accepted: 12/02/2018] [Indexed: 05/21/2023]
Abstract
The pollution of antibiotics and antibiotic resistance genes (ARGs) has been highlighted on a global scale because of their serious threats to the environment and human health. Typical urban water in cities with high population density are ideal mediums for the acquisition and spread of antibiotics and ARGs. The pollution level of a broad range of antibiotics and ARGs in hospital wastewater, groundwater and the Wenyu River, and their fates through three sewage treatment plants (STPs) were investigated in this study. The concentrations of the 11 detected antibiotics ranged from not detected (ND)-16800 ng L-1 in diverse water samples from Beijing, and fluoroquinolones were detected at the highest concentration, especially in the hospital samples. The maximum concentrations of antibiotics in STPs and hospital were 1-3 orders of magnitude higher than those in the surface water from Wenyu River and groundwater. Good removal efficiencies by treatment processes were observed for tetracyclines and quinolones, and low removal efficiencies were observed for sulfonamides and macrolides. These results also revealed that the sulfonamide resistance genes (sul1, sul2) and macrolide resistance genes (ermB) were detected at the highest relative abundances (7.11 × 10-2-1.18 × 10-1) in the water bodies of Beijing. It was worth noting that sul1 abundance was the highest in groundwater samples. The relative abundance of most ARGs in STPs exhibited a declining trend in the order of influent > secondary effluents > effluent. However, the relative abundance of sul 1, sul 2 and tetC in the effluent was higher than those in the influent. The incomplete removal of antibiotics and ARGs in STPs poses a serious threat to the receiving rivers, and affects ecosystem security. Overall, our findings provide favorable support for a further investigation of the spread and risk of antibiotics and ARGs from diverse sources (e.g., STPs and hospitals) to the aquatic environment.
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Affiliation(s)
- Xiaohui Liu
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; School of Environment, Tsinghua University, Beijing, 100084, China
| | - Guodong Zhang
- School of Geography and Environment, Shandong Normal University, Jinan, Shandong, 250358, China
| | - Ying Liu
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Shaoyong Lu
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Pan Qin
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xiaochun Guo
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Bin Bi
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Lei Wang
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Beidou Xi
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Fengchang Wu
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Weiliang Wang
- School of Geography and Environment, Shandong Normal University, Jinan, Shandong, 250358, China
| | - Tingting Zhang
- School of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
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Wu J, Su Y, Deng Y, Guo Z, Cheng C, Ma H, Liu G, Xu L, Feng J. Spatial and temporal variation of antibiotic resistance in marine fish cage-culture area of Guangdong, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 246:463-471. [PMID: 30583154 DOI: 10.1016/j.envpol.2018.12.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/20/2018] [Accepted: 12/09/2018] [Indexed: 06/09/2023]
Abstract
The rapid emergence and dissemination of antibiotic resistance poses a threat to human health and to the marine environment. We have investigated the abundance and diversity of antibiotic resistance genes (ARGs) and of antibiotic-resistant bacteria (ARB), during the seedling period, rearing period, and harvesting period in seven marine fish cage-culture areas in Guangdong. Spatial and temporal variations of AGRs and ARB were also analyzed. Culture-based methods and quantitative PCR were used to detect ARB and ARGs. Bacterial resistance rates were no significantly different within farming periods. The proportion of antibiotic-resistant bacteria was extremely low (average on 1.15%), except for oxytetracycline-resistant bacteria (average on 34.15%). Vibrio was the most common ARB. Sul1, tetB, and ermB, had the highest relative abundance. The abundance of ARGs in the harvesting period was significant highest. The total abundance of ARGs was highest at Raoping and lowest at Dayawan and Liusha. Most ARGs were associated with opportunistic pathogens. The environmental factors effecting ARB and ARGs are complex, and no key factors were identified. This study provides a theoretical basis for assessing the harmfulness of ARGs and ARB to food safety and human health.
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Affiliation(s)
- Jinjun Wu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China; College of Aqua-life Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Youlu Su
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Yiqin Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Zhixun Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Changhong Cheng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Hongling Ma
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Guangfeng Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Liwen Xu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Juan Feng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
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Sim CM, Seong BJ, Kim DW, Kim YB, Wi SG, Kim G, Oh H, Kim T, Chung BY, Song JY, Kim HG, Oh SK, Shin YD, Seok JH, Kang MY, Lee Y, Radebe MJ, Kardjilov N, Honermeier B. Continuous cropping of endangered therapeutic plants via electron beam soil-treatment and neutron tomography. Sci Rep 2018; 8:2136. [PMID: 29391436 PMCID: PMC5794772 DOI: 10.1038/s41598-018-20124-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 01/08/2018] [Indexed: 11/21/2022] Open
Abstract
Various medicinal plants are threatened with extinction owing to their over-exploitation and the prevalence of soil borne pathogens. In this study, soils infected with root-rot pathogens, which prevent continuous-cropping, were treated with an electron beam. The level of soil-borne fungus was reduced to ≤0.01% by soil electron beam treatment without appreciable effects on the levels of antagonistic microorganism or on the physicochemical properties of the soil. The survival rate of 4-year-old plant was higher in electron beam-treated soil (81.0%) than in fumigated (62.5%), virgin (78%), or untreated-replanting soil (0%). Additionally, under various soils conditions, neutron tomography permitted the monitoring of plant health and the detection of root pathological changes over a period of 4-6 years by quantitatively measuring root water content in situ. These methods allow continual cropping on the same soil without pesticide treatment. This is a major step toward the environmentally friendly production of endangered therapeutic herbs.
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Affiliation(s)
- Cheul Muu Sim
- Korea Atomic Energy Research Institute, 1045 Daedeokdaero Yuseong-gu, Daejeon, 303-353, Korea.
- Chungnam National University, 220 Gung-dong, Yuseong-gu, Daejeon, 305-764, Korea.
| | - Bong Jae Seong
- Geumsan Ginseng & Medicinal Crop Experiment Station, Chungnam, 312-831, Korea
| | - Dong Won Kim
- Specialized Crop Research Institute, Jinan gun, Jeonbuk, 567-807, Korea
| | - Yong Bum Kim
- National Institute of Horticulture & Herb Science, Bisani 80, Eumseong, Chungbuk, 389-873, Korea
| | - Seung Gon Wi
- Bioenergy Research Institute, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju, 500-757, Korea
| | - Gyuil Kim
- Institute of Jinan Red Ginseng, Jinan gun, Jeonbuk, 567-801, Korea
| | - Hwasuk Oh
- Korea Atomic Energy Research Institute, 1045 Daedeokdaero Yuseong-gu, Daejeon, 303-353, Korea
- RIC for Next Generation Industrial Radiation Technology, Wonkwang University. 460, Iksan-daero, Iksan-si, Jeollabuk-do, 54538, Korea
| | - TaeJoo Kim
- Korea Atomic Energy Research Institute, 1045 Daedeokdaero Yuseong-gu, Daejeon, 303-353, Korea
| | - Byung Yeoup Chung
- Korea Atomic Energy Research Institute, 1045 Daedeokdaero Yuseong-gu, Daejeon, 303-353, Korea
| | - Jeong Young Song
- Chungnam National University, 220 Gung-dong, Yuseong-gu, Daejeon, 305-764, Korea
| | - Hong Gi Kim
- Chungnam National University, 220 Gung-dong, Yuseong-gu, Daejeon, 305-764, Korea
| | - Sang-Keun Oh
- Chungnam National University, 220 Gung-dong, Yuseong-gu, Daejeon, 305-764, Korea
- Plant Genomics and Breeding Institutes, Seoul National University, Gwanak-gu, Seoul, 151-921, Korea
| | - Young Dol Shin
- GBioMix Institute, 723-1, 2 Palbok-dong, Deokjin-gu, Jeonju, 561-844, Korea
- Chonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju, 561-756, Korea
| | - Jea Hwan Seok
- Chungnam National University, 220 Gung-dong, Yuseong-gu, Daejeon, 305-764, Korea
- GBioMix Institute, 723-1, 2 Palbok-dong, Deokjin-gu, Jeonju, 561-844, Korea
| | - Min Young Kang
- GBioMix Institute, 723-1, 2 Palbok-dong, Deokjin-gu, Jeonju, 561-844, Korea
| | - Yunhee Lee
- GBioMix Institute, 723-1, 2 Palbok-dong, Deokjin-gu, Jeonju, 561-844, Korea
- King's College London, Palace Road, London, SE1 7EH, UK
| | | | | | - Bernd Honermeier
- Justus Liebig University Gießen, Schubertstr. 81, D-35392, Gießen, Germany.
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11
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Wang J, Wang J, Zhao Z, Chen J, Lu H, Liu G, Zhou J, Guan X. PAHs accelerate the propagation of antibiotic resistance genes in coastal water microbial community. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:1145-1152. [PMID: 28886881 DOI: 10.1016/j.envpol.2017.07.067] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 05/11/2023]
Abstract
Antibiotic resistance genes (ARGs) have been regarded as emerging contaminants and have attracted growing attention owing to their widespread presence in the environment. In addition to the well-documented selective pressure of antibiotics, ARGs have also become prevalent because of anthropogenic impacts. Coastal habitats are located between terrestrial and marine ecosystems, which are a hotspot for anthropogenic impacts. Excessive accumulation of polycyclic aromatic hydrocarbons (PAHs) has posed a serious threat to coastal habitats, but no information is available on the effect of PAHs on antibiotic resistance in the microbial community of coastal environments. In this study, the effect of two typical PAHs, naphthalene and phenanthrene, on antibiotic resistance propagation was investigated in a coastal microbial community. The results indicated that the presence of 100 mg/L of naphthalene or 10 mg/L of phenanthrene significantly enhanced the abundance of class I integrase gene (intI1), sulfanilamide resistance gene (sulI), and aminoglycosides resistance gene (aadA2) in the microbial community. Horizontal gene transfer experiment demonstrated that increased abundance of ARGs was primarily a result of conjugative transfer mediated by class I integrons. These findings provided direct evidence that coastal microbial community exposed to PAHs might have resulted in the dissemination of ARGs and implied that a more comprehensive risk assessment of PAHs to natural ecosystems and public health is necessary.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Zelong Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Hong Lu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Guangfei Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaoyan Guan
- Key Lab of Marine Fishery Molecular Biology of Liaoning Province, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
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12
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Singh SK, Ekka R, Mishra M, Mohapatra H. Association study of multiple antibiotic resistance and virulence: a strategy to assess the extent of risk posed by bacterial population in aquatic environment. ENVIRONMENTAL MONITORING AND ASSESSMENT 2017; 189:320. [PMID: 28589461 DOI: 10.1007/s10661-017-6005-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 05/14/2017] [Indexed: 06/07/2023]
Abstract
The present study explored the association between multiple antibiotic resistance (MAR) index and virulence index to determine what percent of environmental antibiotic-resistant (eARB) bacteria could pose threat as potential pathogen. 16srRNA-based sequencing of 113 non-duplicate isolates identified majority of them to be gram negative belonging to Enterobacter, Pseudomonas, Aeromonas, Proteus, Acinetobacter, and Klebsiella. Statistical comparison of MAR indices of the abovementioned genera indicated differences in the median values among the groups (p < 0.001). Pair-wise multiple comparison by Dunn's method indicated significant difference in MAR indices (p < 0.05), based on which multiple antibiotic resistance phenotype could be ranked in the order Pseudomonas > Klebsiella = Acinetobacter > Proteus > Aeromonas > Enterobacter. Association between MAR index and virulence index revealed that 25% of isolates in the population under study posed high threat to human/animal or both; out of which 75% isolates belonged to genus Pseudomonas. Based on observations of comparative analysis of the six gram-negative genera, it could be concluded that Pseudomonas isolates from environment pose significantly high threat as potential pathogens while Enterobacter isolates posed no threat.
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Affiliation(s)
- Santosh Kumar Singh
- School of Biological Sciences, National Institute of Science Education and Research Bhubaneswar, HBNI, Room No. 321, 3rd floor, District-Khurda, Odisha, Jatni, 752050, India
| | - Roseleen Ekka
- School of Biological Sciences, National Institute of Science Education and Research Bhubaneswar, HBNI, Room No. 321, 3rd floor, District-Khurda, Odisha, Jatni, 752050, India
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, Aruna Asafali Marg, Near J.N.U East Gate, New Delhi, 110067, India
| | - Mitali Mishra
- School of Biological Sciences, National Institute of Science Education and Research Bhubaneswar, HBNI, Room No. 321, 3rd floor, District-Khurda, Odisha, Jatni, 752050, India
| | - Harapriya Mohapatra
- School of Biological Sciences, National Institute of Science Education and Research Bhubaneswar, HBNI, Room No. 321, 3rd floor, District-Khurda, Odisha, Jatni, 752050, India.
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13
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Abstract
Antibiotic resistance is a global public health issue of growing proportions. All antibiotics are susceptible to resistance. The evidence is now clear that the environment is the single largest source and reservoir of resistance. Soil, aquatic, atmospheric, animal-associated, and built ecosystems are home to microbes that harbor antibiotic resistance elements and the means to mobilize them. The diversity and abundance of resistance in the environment is consistent with the ancient origins of antibiotics and a variety of studies support a long natural history of associated resistance. The implications are clear: Understanding the evolution of resistance in the environment, its diversity, and mechanisms is essential to the management of our existing and future antibiotic resources.
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Affiliation(s)
- Matthew D Surette
- M.G. DeGroote Institute for Infectious Disease Research and.,Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8N 4K1;
| | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research and.,Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8N 4K1;
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14
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Ben W, Wang J, Cao R, Yang M, Zhang Y, Qiang Z. Distribution of antibiotic resistance in the effluents of ten municipal wastewater treatment plants in China and the effect of treatment processes. CHEMOSPHERE 2017; 172:392-398. [PMID: 28088530 DOI: 10.1016/j.chemosphere.2017.01.041] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/01/2017] [Accepted: 01/05/2017] [Indexed: 05/23/2023]
Abstract
Municipal wastewater treatment plant (WWTP) effluents represent an important contamination source of antibiotic resistance, threatening the ecological safety of receiving environments. In this study, the release of antibiotic resistance to sulfonamides and tetracyclines in the effluents of ten WWTPs in China was investigated. Results indicate that the concentrations of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) ranged from 1.1 × 101 to 8.9 × 103 CFU mL-1 and 3.6 × 101 (tetW) to 5.4 × 106 (tetX) copies mL-1, respectively. There were insignificant correlations of the concentrations of ARB and ARGs with those of corresponding antibiotics. Strong correlations were observed between the total concentrations of tetracycline resistance genes and sulfonamide resistance genes, and both of which were significantly correlated with intI1 concentrations. Statistical analysis of the effluent ARG concentrations in different WWTPs revealed an important role of disinfection in eliminating antibiotic resistance. The release rates of ARB and ARGs through the effluents of ten WWTPs ranged from 5.9 × 1012 to 4.8 × 1015 CFU d-1 and 6.4 × 1012 (tetW) to 1.7 × 1018 (sul1) copies d-1, respectively. This study helps the effective assessment and scientific management of ecological risks induced by antibiotic resistance discharged from WWTPs.
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Affiliation(s)
- Weiwei Ben
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Jian Wang
- Institute of Energy and Environmental Protection, Chinese Academy of Agricultural Engineering, 41 Maizidian Street, Beijing 100125, China; Key Laboratory of Energy Resource Utilization from Agricultural Residues, Ministry of Agriculture, 41 Maizidian Street, Beijing 100125, China
| | - Rukun Cao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Min Yang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Yu Zhang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Zhimin Qiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China.
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15
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Continental-scale pollution of estuaries with antibiotic resistance genes. Nat Microbiol 2017; 2:16270. [DOI: 10.1038/nmicrobiol.2016.270] [Citation(s) in RCA: 608] [Impact Index Per Article: 86.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 12/16/2016] [Indexed: 12/27/2022]
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16
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Tripathi V, Tripathi P. Antibiotic Resistance Genes: An Emerging Environmental Pollutant. PERSPECTIVES IN ENVIRONMENTAL TOXICOLOGY 2017. [DOI: 10.1007/978-3-319-46248-6_9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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17
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McArthur JV, Fletcher DE, Tuckfield RC, Baker-Austin C. Patterns of Multi-Antibiotic-Resistant Escherichia Coli from Streams with No History of Antimicrobial Inputs. MICROBIAL ECOLOGY 2016; 72:840-850. [PMID: 26530280 DOI: 10.1007/s00248-015-0678-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/15/2015] [Indexed: 06/05/2023]
Abstract
A growing body of evidence suggests that contaminated environments may harbor a greater proportion of antibiotic-resistant microorganisms than unpolluted reference sites. Here, we report the screening of 427 Escherichia coli strains isolated from 11 locations on nine streams draining the US Department of Energy's Savannah River Site against a panel of five antibiotics. Streams were chosen to capture a wide range of watersheds from minimally disturbed to highly impacted. Overall, higher levels of resistance were found in waterborne E. coli that also generally exhibited low spatial variability. However, 3 of 11 locations also demonstrated elevated resistance levels in sediments. Two of these occurred in highly disturbed tributaries with no obvious sources of antimicrobials. To further investigate these patterns, we screened a subset of isolates obtained from three streams against 23 antibiotics or antibiotic combinations. A large proportion of these isolates (>40 %) demonstrated resistance to 10 or more antimicrobials, suggesting that environmental multi-antibiotic resistance may be prevalent in this bacterial commensal. Only 4 of 87 viable isolates were tested susceptible to all 23 antibiotics and combinations. Among these multi-antibiotic-resistant isolates, several demonstrated resistance to all structural classes of antimicrobial agents tested, including frontline antibiotics such as gatifloxacin and ciprofloxacin.
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Affiliation(s)
- J V McArthur
- Savannah River Ecology Laboratory, University of Georgia, Drawer E, Aiken, SC, 29802, USA.
| | - D E Fletcher
- Savannah River Ecology Laboratory, University of Georgia, Drawer E, Aiken, SC, 29802, USA
| | | | - C Baker-Austin
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
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18
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Abella J, Bielen A, Huang L, Delmont TO, Vujaklija D, Duran R, Cagnon C. Integron diversity in marine environments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015. [PMID: 26213132 DOI: 10.1007/s11356-015-5085-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Integrons are bacterial genetic elements known to be active vectors of antibiotic resistance among clinical bacteria. They are also found in bacterial communities from natural environments. Although integrons have become especially efficient for bacterial adaptation in the particular context of antibiotic usage, their role in natural environments in other contexts is still unknown. Indeed, most studies have focused on integrons and the spread of antibiotic resistance in freshwater or soil impacted by anthropogenic activities, with only few on marine environments. Notably, integrons show a wider diversity of both gene cassettes and integrase gene in natural environments than in clinical environments, suggesting a general role of integrons in bacterial adaptation. This article reviews the current knowledge on integrons in marine environments. We also present conclusions of our studies on polluted and nonpolluted backgrounds.
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Affiliation(s)
- Justine Abella
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
| | - Ana Bielen
- Laboratory for Molecular Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia
| | - Lionel Huang
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
- Euro Engineering, Technopole Hélioparc Bât Newton, 4 rue Jules Ferry, CS N 99207, 64053, Pau, Cedex 09, France
| | - Tom O Delmont
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biology Laboratory, Woods Hole, MA, USA
| | - Dušica Vujaklija
- Laboratory for Molecular Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Robert Duran
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
| | - Christine Cagnon
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France.
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19
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Abstract
Integrons are versatile gene acquisition systems commonly found in bacterial genomes. They are ancient elements that are a hot spot for genomic complexity, generating phenotypic diversity and shaping adaptive responses. In recent times, they have had a major role in the acquisition, expression, and dissemination of antibiotic resistance genes. Assessing the ongoing threats posed by integrons requires an understanding of their origins and evolutionary history. This review examines the functions and activities of integrons before the antibiotic era. It shows how antibiotic use selected particular integrons from among the environmental pool of these elements, such that integrons carrying resistance genes are now present in the majority of Gram-negative pathogens. Finally, it examines the potential consequences of widespread pollution with the novel integrons that have been assembled via the agency of human antibiotic use and speculates on the potential uses of integrons as platforms for biotechnology.
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20
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Gillings MR, Gaze WH, Pruden A, Smalla K, Tiedje JM, Zhu YG. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME JOURNAL 2014; 9:1269-79. [PMID: 25500508 PMCID: PMC4438328 DOI: 10.1038/ismej.2014.226] [Citation(s) in RCA: 820] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 09/18/2014] [Accepted: 10/23/2014] [Indexed: 12/14/2022]
Abstract
Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.
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Affiliation(s)
- Michael R Gillings
- Department of Biological Sciences, Genes to Geoscience Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Royal Cornwall Hospital, Truro, UK
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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21
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Abstract
Antibiotic resistance has become a problem of global scale. Resistance arises through mutation or through the acquisition of resistance gene(s) from other bacteria in a process called horizontal gene transfer (HGT). While HGT is recognized as an important factor in the dissemination of resistance genes in clinical pathogens, its role in the environment has been called into question by a recent study published in Nature. The authors found little evidence of HGT in soil using a culture-independent functional metagenomics approach, which is in contrast to previous work from the same lab showing HGT between the environment and human microbiome. While surprising at face value, these results may be explained by the lack of selective pressure in the environment studied. Importantly, this work suggests the need for careful monitoring of environmental antibiotic pollution and stringent antibiotic stewardship in the fight against resistance.
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Affiliation(s)
- Julie A Perry
- M. G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
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22
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Koczura R, Semkowska A, Mokracka J. Integron-bearing Gram-negative bacteria in lake waters. Lett Appl Microbiol 2014; 59:514-9. [DOI: 10.1111/lam.12307] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/10/2014] [Accepted: 07/16/2014] [Indexed: 11/28/2022]
Affiliation(s)
- R. Koczura
- Department of Microbiology; Faculty of Biology; Adam Mickiewicz University in Poznań; Poznań Poland
| | - A. Semkowska
- Department of Microbiology; Faculty of Biology; Adam Mickiewicz University in Poznań; Poznań Poland
| | - J. Mokracka
- Department of Microbiology; Faculty of Biology; Adam Mickiewicz University in Poznań; Poznań Poland
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23
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Corno G, Coci M, Giardina M, Plechuk S, Campanile F, Stefani S. Antibiotics promote aggregation within aquatic bacterial communities. Front Microbiol 2014; 5:297. [PMID: 25071728 PMCID: PMC4077313 DOI: 10.3389/fmicb.2014.00297] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 05/29/2014] [Indexed: 11/13/2022] Open
Abstract
The release of antibiotics (AB) into the environment poses several threats for human health due to potential development of AB-resistant natural bacteria. Even though the use of low-dose antibiotics has been promoted in health care and farming, significant amounts of AB are observed in aquatic environments. Knowledge on the impact of AB on natural bacterial communities is missing both in terms of spread and evolution of resistance mechanisms, and of modifications of community composition and productivity. New approaches are required to study the response of microbial communities rather than individual resistance genes. In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses. Bacterial abundance rapidly decreased by 75% in the presence of AB, independently of their concentration, and remained constant until the end of the experiment. The bacterial community was mainly dominated by Aeromonas hydrophila and Brevundimonas intermedia while the other two strains, Micrococcus luteus and Rhodococcus sp. never exceed 10%. Interestingly, the bacterial strains, which were isolated at the end of the experiment, were not AB-resistant, while reassembled communities composed of the 4 strains, isolated from treatments under AB stress, significantly raised their performance (growth rate, abundance) in the presence of AB compared to the communities reassembled with strains isolated from the treatment without AB. By investigating the phenotypic adaptations of the communities subjected to the different treatments, we found that the presence of AB significantly increased co-aggregation by 5-6 fold. These results represent the first observation of co-aggregation as a successful strategy of AB resistance based on phenotype in aquatic bacterial communities, and can represent a fundamental step in the understanding of the effects of AB in aquatic ecosystems.
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Affiliation(s)
- Gianluca Corno
- Microbial Ecology Group, Institute of Ecosystem Study, National Research Council Verbania, Italy
| | - Manuela Coci
- Microbial Ecology Group, Institute of Ecosystem Study, National Research Council Verbania, Italy ; Laboratory of Molecular Microbiology and Antibiotic Resistance, Department of Bio-Medical Sciences, University of Catania Catania, Italy
| | - Marco Giardina
- Microbial Ecology Group, Institute of Ecosystem Study, National Research Council Verbania, Italy ; Laboratory of Molecular Microbiology and Antibiotic Resistance, Department of Bio-Medical Sciences, University of Catania Catania, Italy
| | - Sonia Plechuk
- Microbial Ecology Group, Institute of Ecosystem Study, National Research Council Verbania, Italy ; Laboratory of Molecular Microbiology and Antibiotic Resistance, Department of Bio-Medical Sciences, University of Catania Catania, Italy
| | - Floriana Campanile
- Laboratory of Molecular Microbiology and Antibiotic Resistance, Department of Bio-Medical Sciences, University of Catania Catania, Italy
| | - Stefania Stefani
- Laboratory of Molecular Microbiology and Antibiotic Resistance, Department of Bio-Medical Sciences, University of Catania Catania, Italy
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24
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Vaz-Moreira I, Nunes OC, Manaia CM. Bacterial diversity and antibiotic resistance in water habitats: searching the links with the human microbiome. FEMS Microbiol Rev 2014; 38:761-78. [PMID: 24484530 DOI: 10.1111/1574-6976.12062] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 12/31/2013] [Accepted: 01/10/2014] [Indexed: 12/14/2022] Open
Abstract
Water is one of the most important bacterial habitats on Earth. As such, water represents also a major way of dissemination of bacteria between different environmental compartments. Human activities led to the creation of the so-called urban water cycle, comprising different sectors (waste, surface, drinking water), among which bacteria can hypothetically be exchanged. Therefore, bacteria can be mobilized between unclean water habitats (e.g. wastewater) and clean or pristine water environments (e.g. disinfected and spring drinking water) and eventually reach humans. In addition, bacteria can also transfer mobile genetic elements between different water types, other environments (e.g. soil) and humans. These processes may involve antibiotic resistant bacteria and antibiotic resistance genes. In this review, the hypothesis that some bacteria may share different water compartments and be also hosted by humans is discussed based on the comparison of the bacterial diversity in different types of water and with the human-associated microbiome. The role of such bacteria as potential disseminators of antibiotic resistance and the inference that currently only a small fraction of the clinically relevant antibiotic resistome may be known is discussed.
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Affiliation(s)
- Ivone Vaz-Moreira
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Dr. António Bernardino Almeida, Porto, Portugal
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25
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Varela AR, Manaia CM. Human health implications of clinically relevant bacteria in wastewater habitats. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:3550-3569. [PMID: 23508533 DOI: 10.1007/s11356-013-1594-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 02/25/2013] [Indexed: 06/01/2023]
Abstract
The objective of this review is to reflect on the multiple roles of bacteria in wastewater habitats with particular emphasis on their harmful potential for human health. Indigenous bacteria promote a series of biochemical and metabolic transformations indispensable to achieve wastewater treatment. Some of these bacteria may be pathogenic or harbour antibiotic resistance or virulence genes harmful for human health. Several chemical contaminants (heavy metals, disinfectants and antibiotics) may select these bacteria or their genes. Worldwide studies show that treated wastewater contain antibiotic resistant bacteria or genes encoding virulence or antimicrobial resistance, evidencing that treatment processes may fail to remove efficiently these bio-pollutants. The contamination of the surrounding environment, such as rivers or lakes receiving such effluents, is also documented in several studies. The current state of the art suggests that only some of antibiotic resistance and virulence potential in wastewater is known. Moreover, wastewater habitats may favour the evolution and dissemination of new resistance and virulence genes and the emergence of new pathogens. For these reasons, additional research is needed in order to obtain a more detailed assessment of the long-term effects of wastewater discharges. In particular, it is important to measure the human and environmental health risks associated with wastewater reuse.
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Affiliation(s)
- Ana Rita Varela
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
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Perry JA, Wright GD. The antibiotic resistance "mobilome": searching for the link between environment and clinic. Front Microbiol 2013; 4:138. [PMID: 23755047 PMCID: PMC3667243 DOI: 10.3389/fmicb.2013.00138] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 03/10/2013] [Indexed: 01/30/2023] Open
Abstract
Antibiotic resistance is an ancient problem, owing to the co-evolution of antibiotic-producing and target organisms in the soil and other environments over millennia. The environmental “resistome” is the collection of all genes that directly or indirectly contribute to antibiotic resistance. Many of these resistance determinants originate in antibiotic-producing organisms (where they serve to mediate self-immunity), while others become resistance determinants only when mobilized and over-expressed in non-native hosts (like plasmid-encoded β-lactamases). The modern environmental resistome is under selective pressure from human activities such as agriculture, which may influence the composition of the local resistome and lead to gene transfer events. Beyond the environment, we are challenged in the clinic by the rise in both frequency and diversity of antibiotic resistant pathogens. We assume that clinical resistance originated in the environment, but few examples of direct gene exchange between the environmental resistome and the clinical resistome have been documented. Strong evidence exists to suggest that clinical aminoglycoside and vancomycin resistance enzymes, the extended-spectrum β-lactamase CTX-M and the quinolone resistance gene qnr have direct links to the environmental resistome. In this review, we highlight recent advances in our understanding of horizontal gene transfer of antibiotic resistance genes from the environment to the clinic. Improvements in sequencing technologies coupled with functional metagenomic studies have revealed previously underappreciated diversity in the environmental resistome, and also established novel genetic links to the clinic. Understanding mechanisms of gene exchange becomes vital in controlling the future dissemination of antibiotic resistance.
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Affiliation(s)
- Julie A Perry
- M. G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada ; Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
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Gillings MR. Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome. Front Microbiol 2013; 4:4. [PMID: 23386843 PMCID: PMC3560386 DOI: 10.3389/fmicb.2013.00004] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 01/03/2013] [Indexed: 12/16/2022] Open
Abstract
The widespread use and abuse of antibiotic therapy has evolutionary and ecological consequences, some of which are only just beginning to be examined. One well known consequence is the fixation of mutations and lateral gene transfer (LGT) events that confer antibiotic resistance. Sequential selection events, driven by different classes of antibiotics, have resulted in the assembly of diverse resistance determinants and mobile DNAs into novel genetic elements of ever-growing complexity and flexibility. These novel plasmids, integrons, and genomic islands have now become fixed at high frequency in diverse cell lineages by human antibiotic use. Consequently they can be regarded as xenogenetic pollutants, analogous to xenobiotic compounds, but with the critical distinction that they replicate rather than degrade when released to pollute natural environments. Antibiotics themselves must also be regarded as pollutants, since human production overwhelms natural synthesis, and a major proportion of ingested antibiotic is excreted unchanged into waste streams. Such antibiotic pollutants have non-target effects, raising the general rates of mutation, recombination, and LGT in all the microbiome, and simultaneously providing the selective force to fix such changes. This has the consequence of recruiting more genes into the resistome and mobilome, and of increasing the overlap between these two components of microbial genomes. Thus the human use and environmental release of antibiotics is having second order effects on the microbial world, because these small molecules act as drivers of bacterial evolution. Continued pollution with both xenogenetic elements and the selective agents that fix such elements in populations has potentially adverse consequences for human welfare.
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Affiliation(s)
- Michael R Gillings
- Department of Biological Sciences, Macquarie University Sydney, NSW, Australia
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Marti E, Balcázar JL. Antibiotic Resistance in the Aquatic Environment. ANALYSIS, REMOVAL, EFFECTS AND RISK OF PHARMACEUTICALS IN THE WATER CYCLE - OCCURRENCE AND TRANSFORMATION IN THE ENVIRONMENT 2013. [DOI: 10.1016/b978-0-444-62657-8.00019-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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