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S V, T J, E AP, A MHA. Antibiotic resistance of heterotrophic bacteria from the sediments of adjoining high Arctic fjords, Svalbard. Braz J Microbiol 2024:10.1007/s42770-024-01368-0. [PMID: 38767750 DOI: 10.1007/s42770-024-01368-0] [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: 12/30/2023] [Accepted: 04/08/2024] [Indexed: 05/22/2024] Open
Abstract
Antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) are now considered major global threats. The Kongsfjorden and Krossfjorden are the interlinked fjords in the Arctic that are currently experiencing the effects of climate change and receiving input of pollutants from distant and regional sources. The present study focused on understanding the prevalence of antibiotic resistance of retrievable heterotrophic bacteria from the sediments of adjacent Arctic fjords Kongsfjorden and Krossfjorden. A total of 237 bacterial isolates were tested against 16 different antibiotics. The higher resistance observed towards Extended Spectrum β-lactam antibiotic (ESBL) includes ceftazidime (45.56%) followed by trimethoprim (27%) and sulphamethizole (24.05%). The extent of resistance was meagre against tetracycline (2.53%) and gentamycin (2.95%). The 16S rRNA sequencing analysis identified that Proteobacteria (56%) were the dominant antibiotic resistant phyla, followed by Firmicutes (35%), Actinobacteria (8%) and Bacteroidetes. The dominant resistant bacterial isolates are Bacillus cereus (10%), followed by Alcaligenes faecalis (6.47%), Cytobacillus firmus (5.75%) Salinibacterium sp. (5%) and Marinobacter antarcticus (5%). Our study reveals the prevalence of antibiotic resistance showed significant differences in both the inner and outer fjords of Kongsfjorden and Krossfjorden (p < 0.05). This may be the input of antibiotic resistance bacteria released into the fjords from the preserved permafrost due to the melting of glaciers, horizontal gene transfer, and human influence in the Arctic region act as a selection pressure for the development and dissemination of more antibiotic resistant bacteria in Arctic fjords.
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Affiliation(s)
- Vishnupriya S
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, India.
| | - Jabir T
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, 403 804, Vasco- da-Gama, Goa, India
| | - Akhil Prakash E
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, India
| | - Mohamed Hatha A A
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, India
- CUSAT NCPOR Centre for Polar Sciences, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, India
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2
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Gattinger D, Schlenz V, Weil T, Sattler B. From remote to urbanized: Dispersal of antibiotic-resistant bacteria under the aspect of anthropogenic influence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171532. [PMID: 38458439 DOI: 10.1016/j.scitotenv.2024.171532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Antibiotic resistance is a growing global concern, but our understanding of the spread of resistant bacteria in remote regions remains limited. While some level of intrinsic resistance likely contributes to reduced susceptibility to antimicrobials in the environment, it is evident that human actions, particularly the (mis)use of antibiotics, play a significant role in shaping the environmental resistome, even in seemingly distant habitats like glacier ice sheets. Our research aims to bridge this knowledge gap by investigating the direct influence of human activities on the presence of antibiotic-resistant bacteria in various habitats. To achieve a comprehensive assessment of anthropogenic impact across diverse and seemingly isolated sampling sites, we developed an innovative approach utilizing Corine Land Cover data and heatmaps generated from sports activity trackers. This method allowed us to make meaningful comparisons across relatively pristine environments. Our findings indicate a noteworthy increase in culturable antibiotic-resistant bacteria with heightened human influence, as evidenced by our analysis of glacier, snow, and lake water samples. Notably, the most significant concentrations of antibiotic-resistant and multidrug-resistant microorganisms were discovered in two highly impacted sampling locations, namely the Tux Glacier and Gas Station Ellmau.
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Affiliation(s)
- Daniel Gattinger
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria.
| | - Valentin Schlenz
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Tobias Weil
- Research and Innovation Centre, Fondazione Edmund Mach, All'adige, Italy
| | - Birgit Sattler
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria; Austrian Polar Research Institute, Vienna, Austria
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3
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Makowska-Zawierucha N, Trzebny A, Zawierucha K, Manthapuri V, Bradley JA, Pruden A. Arctic plasmidome analysis reveals distinct relationships among associated antimicrobial resistance genes and virulence genes along anthropogenic gradients. GLOBAL CHANGE BIOLOGY 2024; 30:e17293. [PMID: 38687495 DOI: 10.1111/gcb.17293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/30/2024] [Accepted: 03/30/2024] [Indexed: 05/02/2024]
Abstract
Polar regions are relatively isolated from human activity and thus could offer insight into anthropogenic and ecological drivers of the spread of antibiotic resistance. Plasmids are of particular interest in this context given the central role that they are thought to play in the dissemination of antibiotic resistance genes (ARGs). However, plasmidomes are challenging to profile in environmental samples. The objective of this study was to compare various aspects of the plasmidome associated with glacial ice and adjacent aquatic environments across the high Arctic archipelago of Svalbard, representing a gradient of anthropogenic inputs and specific treated and untreated wastewater outflows to the sea. We accessed plasmidomes by applying enrichment cultures, plasmid isolation and shotgun Illumina sequencing of environmental samples. We examined the abundance and diversity of ARGs and other stress-response genes that might be co/cross-selected or co-transported in these environments, including biocide resistance genes (BRGs), metal resistance genes (MRGs), virulence genes (VGs) and integrons. We found striking differences between glacial ice and aquatic environments in terms of the ARGs carried by plasmids. We found a strong correlation between MRGs and ARGs in plasmids in the wastewaters and fjords. Alternatively, in glacial ice, VGs and BRGs genes were dominant, suggesting that glacial ice may be a repository of pathogenic strains. Moreover, ARGs were not found within the cassettes of integrons carried by the plasmids, which is suggestive of unique adaptive features of the microbial communities to their extreme environment. This study provides insight into the role of plasmids in facilitating bacterial adaptation to Arctic ecosystems as well as in shaping corresponding resistomes. Increasing human activity, warming of Arctic regions and associated increases in the meltwater run-off from glaciers could contribute to the release and spread of plasmid-related genes from Svalbard to the broader pool of ARGs in the Arctic Ocean.
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Affiliation(s)
- Nicoletta Makowska-Zawierucha
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Artur Trzebny
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Vineeth Manthapuri
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - James A Bradley
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO, Marseille, France
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
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4
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Ren Z, Zhang C, Li X, Luo W. Thermokarst lakes are hotspots of antibiotic resistance genes in permafrost regions on the Qinghai-Tibet Plateau. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 344:123334. [PMID: 38218544 DOI: 10.1016/j.envpol.2024.123334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/02/2023] [Accepted: 01/07/2024] [Indexed: 01/15/2024]
Abstract
Antibiotic resistance genes (ARGs) are natural products and emerging pollutants in remote environments, including permafrost regions that are rapidly thawing due to climate warming. We investigated the role of thermokarst lakes (including sediment and water) in reserving ARGs compared to permafrost soils across the permafrost regions on the Qinghai-Tibet Plateau. As intrinsically connected distinct environments, permafrost soil, lake sediment, and lake water harbored 1239 ARGs in total, while a considerable number of same ARGs (683 out of 1239) concurrently presented in all these environments. Soil and sediment had a higher number of ARGs than water. Multidrug resistance genes were the most diverse and abundant in all three environments, where cls, ropB, mdfA, fabI, and macB were the top five most abundant ARGs while with different orders. Soil and sediment had similar ARG profiles, and the alpha and beta diversity of ARGs in sediment were positively correlated with that in soil. The beta diversity of ARG profiles between sediment and soil was highly contributed by turnover component (89%). However, turnover and nestedness components were almost equality contributed (46%-54%) to the beta diversity of ARG profiles between soil and water as well as between sediment and water. The results suggested that thermokarst lake sediments might inherit the ARGs in permafrost soils. Water ARGs are the subset of soil ARGs and sediment ARGs to a certain degree with species turnover playing a significant role. When accounting the ARGs in sediment and water together, thermokarst lakes had a significantly higher number of ARGs than permafrost soils, suggesting that thermokarst lakes act as the hotspots of ARGs in permafrost regions. These findings are disturbing especially due to the fact that tremendous number of thermokarst lakes are forming under accelerating climate change.
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Affiliation(s)
- Ze Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Cheng Zhang
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, 519087, China; School of Engineering Technology, Beijing Normal University, Zhuhai, 519087, China
| | - Xia Li
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Wei Luo
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, 200136, China; Key Laboratory of Polar Ecosystem and Climate Change (Shanghai Jiao Tong University), Ministry of Education, Shanghai, 200030, China; The Technology and Equipment Engineering Centre for Polar Observations, Zhejiang University, Zhoushan, 316000, China.
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5
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Arnold KE, Laing G, McMahon BJ, Fanning S, Stekel DJ, Pahl O, Coyne L, Latham SM, McIntyre KM. The need for One Health systems-thinking approaches to understand multiscale dissemination of antimicrobial resistance. Lancet Planet Health 2024; 8:e124-e133. [PMID: 38331529 DOI: 10.1016/s2542-5196(23)00278-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/29/2023] [Accepted: 12/15/2023] [Indexed: 02/10/2024]
Abstract
Although the effects of antimicrobial resistance (AMR) are most obvious at clinical treatment failure, AMR evolution, transmission, and dispersal happen largely in environmental settings, for example within farms, waterways, livestock, and wildlife. We argue that systems-thinking, One Health approaches are crucial for tackling AMR, by understanding and predicting how anthropogenic activities interact within environmental subsystems, to drive AMR emergence and transmission. Innovative computational methods integrating big data streams (eg, from clinical, agricultural, and environmental monitoring) will accelerate our understanding of AMR, supporting decision making. There are challenges to accessing, integrating, synthesising, and interpreting such complex, multidimensional, heterogeneous datasets, including the lack of specific metrics to quantify anthropogenic AMR. Moreover, data confidentiality, geopolitical and cultural variation, surveillance gaps, and science funding cause biases, uncertainty, and gaps in AMR data and metadata. Combining systems-thinking with modelling will allow exploration, scaling-up, and extrapolation of existing data. This combination will provide vital understanding of the dynamic movement and transmission of AMR within and among environmental subsystems, and its effects across the greater system. Consequently, strategies for slowing down AMR dissemination can be modelled and compared for efficacy and cost-effectiveness.
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Affiliation(s)
- Kathryn E Arnold
- Department of Environment and Geography, University of York, York, UK.
| | | | - Barry J McMahon
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Dublin, Ireland
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK; Department of Mathematics and Applied Mathematics, University of Johannesburg, Johannesburg, South Africa
| | - Ole Pahl
- Department of Civil Engineering and Environmental Management, School of Computing, Engineering and Built Environment, Glasgow Caledonian University, Glasgow, UK
| | - Lucy Coyne
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; National Office of Animal Health, Stevenage, UK
| | - Sophia M Latham
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - K Marie McIntyre
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Modelling, Evidence and Policy group, School of Natural and Environmental Sciences, Newcastle University, Newcastle, UK
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6
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Ren Z, Gao H. Antibiotic resistance genes in integrated surface ice, cryoconite, and glacier-fed stream in a mountain glacier in Central Asia. ENVIRONMENT INTERNATIONAL 2024; 184:108482. [PMID: 38324929 DOI: 10.1016/j.envint.2024.108482] [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: 12/04/2023] [Revised: 01/16/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Glacier ice, cryoconite, and glacier-fed streams are interconnected features that have important implications for the dynamics and distribution of abiotic and biotic materials. However, the presence and behavior of antibiotic resistance genes (ARGs) within these glacial environments remained largely unexplored. Addressing this gap, we hypothesized that ARGs are widely distributed and exhibit distinct yet interconnected patterns of diversity and dynamics in these glacial environments. Here, we investigated ARGs in a mountain glacier in Central Asia. A total of 944 ARGs, spanning 22 antibiotic classes, were identified, with 633 ARGs shared across all three environments. Cryoconite exhibited the highest ARG richness, followed by ice, while stream biofilm displayed the lowest value. Exploring ARG profiles, we observed a consistent pattern in terms of antibiotic class and resistance mechanism across all three environments. Beta-lactam resistance genes exhibited the highest diversity, followed by multidrug, glycopeptide, and MLS. The predominant mechanisms were antibiotic inactivation, antibiotic efflux, and target alteration. The most prevalent ARG is cls, followed by mdfA, ropB, fabI, and macB. The similarity in ARG profiles between surface ice and cryoconite samples was more pronounced than their resemblance to stream biofilm samples. The variations of ARG profiles between any pair of environments were largely contributed by turnover component. Further insights into microbial interactions revealed 2328 significant associations between 80 OTUs and 356 ARGs, indicating complex relationships. Certain OTUs, including those from the genera Polaromonas, Ferruginibacter, Hymenobacter, Phormidesmis, Novosphingobium, and Polymorphobacter, were speculated as potential hosts for a variety of ARGs. Our findings underscore the intricate dynamics of antibiotic resistance in glacial ecosystems, emphasizing the need for a holistic understanding of ARG distribution, diversity, and associations across diverse environmental compartments. This research contributes valuable insights into the potential ecological implications of antibiotic resistance dissemination in cold environments, particularly as influenced by increasing climate change.
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Affiliation(s)
- Ze Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hongkai Gao
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China.
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7
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Stevenson EM, Buckling A, Cole M, Lindeque PK, Murray AK. Selection for antimicrobial resistance in the plastisphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168234. [PMID: 37924893 DOI: 10.1016/j.scitotenv.2023.168234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/20/2023] [Accepted: 10/29/2023] [Indexed: 11/06/2023]
Abstract
Microplastics and antimicrobials are widespread contaminants that threaten global systems and frequently co-exist in the presence of human or animal pathogens. Whilst the impact of each of these contaminants has been studied in isolation, the influence of this co-occurrence in driving antimicrobial resistance (AMR)1 in microplastic-adhered microbial communities, known as 'the Plastisphere', is not well understood. This review proposes the mechanisms by which interactions between antimicrobials and microplastics may drive selection for AMR in the Plastisphere. These include: 1) increased rates of horizontal gene transfer in the Plastisphere compared with free-living counterparts and natural substrate controls due to the proximity of cells, co-occurrence of environmental microplastics with AMR selective compounds and the sequestering of extracellular antibiotic resistance genes in the biofilm matrix. 2) An elevated AMR selection pressure in the Plastisphere due to the adsorbing of AMR selective or co-selective compounds to microplastics at concentrations greater than those found in surrounding mediums and potentially those adsorbed to comparator particles. 3) AMR selection pressure may be further elevated in the Plastisphere due to the incorporation of antimicrobial or AMR co-selective chemicals in the plastic matrix during manufacture. Implications for both ecological functioning and environmental risk assessments are discussed, alongside recommendations for further research.
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Affiliation(s)
- Emily M Stevenson
- European Centre for Environment and Human Health, Environment and Sustainability Institute, University of Exeter Medical School, Faculty of Health and Life Sciences, Penryn Campus, Cornwall, UK; Marine Ecology & Biodiversity, Plymouth Marine Laboratory, Prospect Place, West Hoe, Plymouth PL1 3DH, UK; Faculty of Environment, Science and Economy, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| | - Angus Buckling
- Faculty of Environment, Science and Economy, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| | - Matthew Cole
- Marine Ecology & Biodiversity, Plymouth Marine Laboratory, Prospect Place, West Hoe, Plymouth PL1 3DH, UK
| | - Penelope K Lindeque
- Marine Ecology & Biodiversity, Plymouth Marine Laboratory, Prospect Place, West Hoe, Plymouth PL1 3DH, UK; Faculty of Environment, Science and Economy, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| | - Aimee K Murray
- European Centre for Environment and Human Health, Environment and Sustainability Institute, University of Exeter Medical School, Faculty of Health and Life Sciences, Penryn Campus, Cornwall, UK.
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8
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Wu L, Wang M, Rong L, Wang W, Chen L, Wu Q, Sun H, Huang X, Zou X. Structural effects of sulfonamides on the proliferation dynamics of sulfonamide resistance genes in the sequencing batch reactors and the mechanism. J Environ Sci (China) 2024; 135:161-173. [PMID: 37778792 DOI: 10.1016/j.jes.2022.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 10/03/2023]
Abstract
Antibiotic resistance genes (ARGs) can be easily promoted by antibiotics, however, the structural effects of antibiotics on the proliferation of ARGs dynamic and the associated mechanisms remain obscure in, especially, activated sludge sequencing batch reactors. In the present study, the effects of 9 sulfonamides (SAs) with different structures on the proliferation dynamic of sulfonamide resistance genes (Suls) in the activated sludge sequencing batch reactors and the corresponding mechanisms were determined (30 days), and the results showed that the largest proliferation value (∆AR) of Suls dynamic for SAs (sulfachloropyridazine) was approximately 2.9 times than that of the smallest one (sulfadiazine). The proliferation of Suls was significantly related to the structural features (minHBint6, SssNH, SHBd and SpMax2_Bhm) that represent the biological activity of SAs. To interpret the phenomenon, a mechanistic model was developed and the results indicated that the biodegradation of SAs (T1/2) rather than conjugative transfer frequency or mutation frequency tends to be the key process for affecting Suls proliferation. T1/2 was proved to be dependent on the interactions between SAs and receptors (Ebinding), the cleavage mode (bond dissociation energy), and the site of nucleophilic assault. Besides, the metagenomic analysis showed that SAs posed significant effect on antibiotic resistome and Tnp31 played a vital role in the proliferation of Suls. Overall, our findings provide important insight into a theoretical basis for understanding the structural effects of SAs on the proliferation of ARGs in SBR systems.
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Affiliation(s)
- Ligui Wu
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Mingyu Wang
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Lingling Rong
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Wenbiao Wang
- Key Laboratory of Organic Compound Pollution Control Engineering (MOE), School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Linwei Chen
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Qiaofeng Wu
- Fuzhou Urban and Rural Construction Group Co. Ltd., Fuzhou 350007, China
| | - Haoyu Sun
- Key Laboratory of Organic Compound Pollution Control Engineering (MOE), School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Xiangfeng Huang
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Xiaoming Zou
- School of Life Science, Jinggangshan University, Ji'an 343009, China.
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9
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Wei F, Xia H, Huang K, Wei C. Exogenous mobile genetic elements and their associated integrons drive the enrichment of antibiotic-resistant genes in the river of a valley basin city (Lanzhou, China). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:3195-3206. [PMID: 38085475 DOI: 10.1007/s11356-023-31269-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 11/23/2023] [Indexed: 01/18/2024]
Abstract
River is a unique source of drinking water in valley-type cities, affecting local urban development and human lifestyles. However, the key driving factors for dissemination of antibiotic-resistant genes (ARGs) in valley-type urban environments remain unclear. This study aimed to investigate the distribution of ARGs in the Yellow River and to clarify the driving factors of ARGs in a typical valley basin city (Lanzhou, China). The seven selected ARGs with higher abundances including tetracycline resistance genes (tetM, tetX), macrolide resistance genes (ermB, ermF, ereA), and sulfonamide resistance genes (sul1, sul2) were detected. The results showed that the total absolute abundance of all the selected ARGs varied from 9.97 × 1012 to 1.04 × 1015 copies/L in the water body, with higher abundances in the wet season, relative to the dry season. Among these, sulfonamide resistance genes (sul1, sul2) displayed the highest absolute abundance in the river and soil. The ARGs and mobile genetic elements (MGEs) were significantly correlated with bacterial abundance, dissolved organic carbon (DOC), ammonia nitrogen (NH4+), and total nitrogen (TN) levels in the water environment (Mantel test, P < 0.01). Structural equation modeling revealed the direct input of point-source and nonpoint-source ARGs in this area contributed less to the overall level of the ARGs in the water. Among the multiple drivers, the MGEs derived from wastewater treatment plant and anthropogenic nonpoint area positively and directly affected the ARG profiles in water (P < 0.01), rather than the factors of bacterial abundance and physicochemical properties. According to this study, the exogenous MGEs from anthropogenic activities are the main driver for the enrichment of ARGs in the valley-type urban river environment.
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Affiliation(s)
- Fengyi Wei
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Hui Xia
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Kui Huang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China.
- Key Laboratory of Yellow River Water Environment in Gansu Province, Lanzhou, 730070, China.
| | - Chengchen Wei
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
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10
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Shen Y, Liu Y, Du Y, Wang X, Guan J, Jia X, Xu F, Song Z, Gao H, Zhang B, Guo P. Transfer of antibiotic resistance genes from soil to wheat: Role of host bacteria, impact on seed-derived bacteria, and affecting factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167279. [PMID: 37741386 DOI: 10.1016/j.scitotenv.2023.167279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
The transfer of antibiotic resistance genes (ARGs) from soils to plants is poorly understood, especially the role of host bacteria in soils and its impact on seed-derived bacteria. Wheat (Triticum aestivum L.) was thus used to fill the gap by conducting pot experiments, with target ARGs and bacterial community analyzed. Results showed that the relative abundances of target ARGs gradually decreased during transfer of ARGs from the rhizosphere soil to root and shoot. Host bacteria in the rhizosphere soil were the primary source of ARGs in wheat. The 38, 21, and 19 potential host bacterial genera of target ARGs and intI1 in the rhizosphere soil, root, and shoot were identified, respectively, and they mainly belonged to phylum Proteobacteria. The abundance of ARGs carried by pathogenic Corynebacterium was reduced in sequence. During transfer of ARGs from the rhizosphere soil to root and shoot, some seed-derived bacteria and pathogenic Acinetobacter obtained ARGs through horizontal gene transfer and became potential host bacteria. Furthermore, total organic carbon, available nitrogen of the rhizosphere soil, water use efficiency, vapor pressure deficit, and superoxide dismutase of plants were identified as the key factors affecting potential host bacteria transfer in soils to wheat. This work provides important insights into transfer of ARGs and deepens our understanding of potential health risks of ARGs from soils to plants.
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Affiliation(s)
- Yanping Shen
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Yibo Liu
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Yutong Du
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Xu Wang
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Jiunian Guan
- School of Environment, Northeast Normal University, Changchun 130117, PR China
| | - Xiaohui Jia
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Fukai Xu
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Ziwei Song
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Hongjie Gao
- Chinese Research Academy of Environmental Science, Beijing 100012, PR China.
| | - Baiyu Zhang
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada.
| | - Ping Guo
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China.
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11
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Abstract
Antibiotic resistance genes predate the therapeutic uses of antibiotics. However, the current antimicrobial resistance crisis stems from our extensive use of antibiotics and the generation of environmental stressors that impose new selective pressure on microbes and drive the evolution of resistant pathogens that now threaten human health. Similar to climate change, this global threat results from human activities that change habitats and natural microbiomes, which in turn interact with human-associated ecosystems and lead to adverse impacts on human health. Human activities that alter our planet at global scales exacerbate the current resistance crisis and exemplify our central role in large-scale changes in which we are both protagonists and architects of our success but also casualties of unanticipated collateral outcomes. As cognizant participants in this ongoing planetary experiment, we are driven to understand and find strategies to curb the ongoing crises of resistance and climate change.
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Affiliation(s)
- María Mercedes Zambrano
- Corpogen Research Center, Bogotá, Colombia;
- Dirección de Investigaciones y Transferencia de Conocimiento, Universidad Central, Bogotá, Colombia
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12
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Naidoo Y, Pierneef RE, Cowan DA, Valverde A. Characterization of the soil resistome and mobilome in Namib Desert soils. Int Microbiol 2023:10.1007/s10123-023-00454-x. [PMID: 37968548 DOI: 10.1007/s10123-023-00454-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023]
Abstract
The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.
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Affiliation(s)
- Yashini Naidoo
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
| | - Rian E Pierneef
- Biotechnology Platform, Agricultural Research Council, Soutpan Road, Onderstepoort Campus, Pretoria, 0110, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Angel Valverde
- IRNASA-CSIC, Cordel de Merinas, 37008, Salamanca, Spain.
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13
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Saab ME, Vanier G, Sudlovenick E, Powell AL, Simonee J, Desmarais G, Muckle CA, Fairbrother JM, Daoust PY. Occurrence and antimicrobial resistance of Salmonella species and potentially pathogenic Escherichia coli in free-living seals of Canadian Atlantic and eastern Arctic waters. Zoonoses Public Health 2023; 70:542-554. [PMID: 37317052 DOI: 10.1111/zph.13064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 05/10/2023] [Accepted: 05/27/2023] [Indexed: 06/16/2023]
Abstract
Seal populations in Canadian waters provide sustenance to coastal communities. There is potential for pathogenic and/or antimicrobial-resistant bacteria to transfer to humans through inadvertent faecal contamination of seal products. The objective of this study was to investigate the occurrence and potential antimicrobial resistance of Salmonella spp., Escherichia coli and Listeria monocytogenes in faecal samples collected from grey seals (Halichoerus grypus) in the Gulf of St. Lawrence and from ringed seals (Pusa hispida) in Frobisher Bay and Eclipse Sound, Nunavut, Canada. Grey seals were harvested during commercial hunts or during scientific sampling; ringed seals were collected by Inuit hunters during subsistence harvests. Virulence genes defining pathogenic E. coli were identified by PCR, and antimicrobial susceptibility testing was performed on recovered isolates. In grey seals, E. coli was detected in 34/44 (77%) samples, and pathogenic E. coli (extraintestinal E. coli [ExPEC], enteropathogenic E. coli [EPEC] or ExPEC/EPEC) was detected in 13/44 (29%) samples. Non-susceptibility to beta-lactams and quinolones was observed in isolates from 18 grey seals. In ringed seals from Frobisher Bay, E. coli was detected in 4/45 (9%) samples; neither virulence genes nor antimicrobial resistance was detected in these isolates. In ringed seals from Eclipse Sound, E. coli was detected in 8/50 (16%) samples and pathogenic E. coli (ExPEC and ExPEC/EPEC) in 5/50 (10%) samples. One seal from Eclipse Sound had an E. coli isolate resistant to beta-lactams. A monophasic Salmonella Typhimurium was recovered from 8/50 (16%) seals from Eclipse Sound. All Salmonella isolates were resistant to ampicillin, streptomycin, sulfisoxazole and tetracycline. L. monocytogenes was not detected in any sample. These findings suggest that seals may act as important sentinel species and as reservoirs or vectors for antimicrobial-resistant and virulent E. coli and Salmonella species. Further characterization of these isolates would provide additional insights into the source and spread of antimicrobial resistance and virulence genes in these populations of free-living seals.
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Affiliation(s)
- Matthew E Saab
- Diagnostic Services, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Ghyslaine Vanier
- WOAH Reference Laboratory for Escherichia coli, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Enooyaq Sudlovenick
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Ashley Lora Powell
- Diagnostic Services, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | | | - Gabriel Desmarais
- WOAH Reference Laboratory for Escherichia coli, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Catherine Anne Muckle
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - John Morris Fairbrother
- WOAH Reference Laboratory for Escherichia coli, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Pierre-Yves Daoust
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
- Canadian Wildlife Health Cooperative, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
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14
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Gattinger D, Pichler K, Weil T, Sattler B. A comparative approach to confirm antibiotic-resistant microbes in the cryosphere. Front Microbiol 2023; 14:1212378. [PMID: 37601352 PMCID: PMC10435281 DOI: 10.3389/fmicb.2023.1212378] [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: 04/26/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023] Open
Abstract
Antibiotic-resistant microbes pose one of the biggest challenges of the current century. While areas with proximity to human impact are closely studied, a lot is yet to learn about antimicrobial resistance in remote regions like the cryosphere. Nowadays, antibiotic (AB) resistance is considered a pollution that has reached the Earth's most pristine areas. However, monitoring of resistant environmental bacteria therein faces several challenges that inhibit scientific progress in this field. Due to many cultivation-based antibiotic susceptibility tests being optimized for mesophilic pathogenic microorganisms, many researchers opt for expensive molecular biological approaches to detect antibiotic resistance in the cryosphere. However, some disadvantages of these methods prohibit effective comprehensive monitoring of resistant bacteria in pristine areas, hence we suggest established cultivation-based approaches when looking for antimicrobial resistance in the cryosphere. In this study, we compared two common antibiotic susceptibility tests and optimized them to meet the needs of psychrophilic microorganisms. The resulting cultures thereof originated from cryospheric habitats with differing anthropogenic impacts. The results show that these methods are applicable to detect antibiotic resistance in cryospheric habitats and could potentially increase the comparability between studies.
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Affiliation(s)
- Daniel Gattinger
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Katrin Pichler
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Tobias Weil
- Research and Innovation Centre, Fondazione Edmund Mach, All'adige, Italy
| | - Birgit Sattler
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
- Austrian Polar Research Institute, Vienna, Austria
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15
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Bengtsson-Palme J, Abramova A, Berendonk TU, Coelho LP, Forslund SK, Gschwind R, Heikinheimo A, Jarquín-Díaz VH, Khan AA, Klümper U, Löber U, Nekoro M, Osińska AD, Ugarcina Perovic S, Pitkänen T, Rødland EK, Ruppé E, Wasteson Y, Wester AL, Zahra R. Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs? ENVIRONMENT INTERNATIONAL 2023; 178:108089. [PMID: 37441817 DOI: 10.1016/j.envint.2023.108089] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Antimicrobial resistance (AMR) is a global threat to human and animal health and well-being. To understand AMR dynamics, it is important to monitor resistant bacteria and resistance genes in all relevant settings. However, while monitoring of AMR has been implemented in clinical and veterinary settings, comprehensive monitoring of AMR in the environment is almost completely lacking. Yet, the environmental dimension of AMR is critical for understanding the dissemination routes and selection of resistant microorganisms, as well as the human health risks related to environmental AMR. Here, we outline important knowledge gaps that impede implementation of environmental AMR monitoring. These include lack of knowledge of the 'normal' background levels of environmental AMR, definition of high-risk environments for transmission, and a poor understanding of the concentrations of antibiotics and other chemical agents that promote resistance selection. Furthermore, there is a lack of methods to detect resistance genes that are not already circulating among pathogens. We conclude that these knowledge gaps need to be addressed before routine monitoring for AMR in the environment can be implemented on a large scale. Yet, AMR monitoring data bridging different sectors is needed in order to fill these knowledge gaps, which means that some level of national, regional and global AMR surveillance in the environment must happen even without all scientific questions answered. With the possibilities opened up by rapidly advancing technologies, it is time to fill these knowledge gaps. Doing so will allow for specific actions against environmental AMR development and spread to pathogens and thereby safeguard the health and wellbeing of humans and animals.
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Affiliation(s)
- Johan Bengtsson-Palme
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) in Gothenburg, Sweden.
| | - Anna Abramova
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) in Gothenburg, Sweden
| | - Thomas U Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Zellescher Weg 40, 01217 Dresden, Germany
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rémi Gschwind
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME F-75018 Paris, France
| | - Annamari Heikinheimo
- University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O.Box 66, FI-00014, Finland; Finnish Food Authority, P.O.Box 100, 00027 Seinäjoki, Finland
| | - Víctor Hugo Jarquín-Díaz
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Ayaz Ali Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Department of Biotechnology, University of Malakand, Chakdara, Dir (Lower), Khyber Pakhtunkhwa, Pakistan
| | - Uli Klümper
- Institute of Hydrobiology, Technische Universität Dresden, Zellescher Weg 40, 01217 Dresden, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Marmar Nekoro
- Swedish Knowledge Centre on Pharmaceuticals in the Environment, Swedish Medical Products Agency, P.O Box 26, 751 03 Uppsala, Sweden
| | - Adriana D Osińska
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, P.O.Box 5003 NMBU, N-1432 Ås, Norway
| | - Svetlana Ugarcina Perovic
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Tarja Pitkänen
- University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O.Box 66, FI-00014, Finland; Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O.Box 95, FI-70701 Kuopio, Finland
| | | | - Etienne Ruppé
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME F-75018 Paris, France
| | - Yngvild Wasteson
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, P.O.Box 5003 NMBU, N-1432 Ås, Norway
| | | | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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16
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Marutescu LG. Current and Future Flow Cytometry Applications Contributing to Antimicrobial Resistance Control. Microorganisms 2023; 11:1300. [PMID: 37317273 DOI: 10.3390/microorganisms11051300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023] Open
Abstract
Antimicrobial resistance is a global threat to human health and welfare, food safety, and environmental health. The rapid detection and quantification of antimicrobial resistance are important for both infectious disease control and public health threat assessment. Technologies such as flow cytometry can provide clinicians with the early information, they need for appropriate antibiotic treatment. At the same time, cytometry platforms facilitate the measurement of antibiotic-resistant bacteria in environments impacted by human activities, enabling assessment of their impact on watersheds and soils. This review focuses on the latest applications of flow cytometry for the detection of pathogens and antibiotic-resistant bacteria in both clinical and environmental samples. Novel antimicrobial susceptibility testing frameworks embedding flow cytometry assays can contribute to the implementation of global antimicrobial resistance surveillance systems that are needed for science-based decisions and actions.
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Affiliation(s)
- Luminita Gabriela Marutescu
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, 91-95 Spl. Independentei, 050095 Bucharest, Romania
- Research Institute of the University of Bucharest, 050095 Bucharest, Romania
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17
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Wang T, Zhang W, Liao G, Zhang M, Li L, Wang D. Occurrence and influencing factors of antibiotics and antibiotic resistance genes in sediments of the largest multi-habitat lakes in Northern China. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:2567-2578. [PMID: 36057679 DOI: 10.1007/s10653-022-01377-8] [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: 04/13/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Baiyangdian Lake is a typical and largest multi-habitat lake in the North plain of China. To understand the generation and transmission of antibiotics resistance genes (ARGs) in multi-habitat lakes, the contents of nutrients (TC, TOC, TN, TP and TS), heavy metals (Zn, Cr, Ni, Cu, Pb, As, Cd and Hg), 22 antibiotics, 16S-rRNA(16S), Class I integron (intI1) and 20 ARGs were determined. Samples were taken from the Fuhe river, river estuaries, reed marshes, living area, fish ponds and open water of Baiyangdian Lake. The results showed that quinolones were the main pollutants in six habitats, and the content range was ND-104.94 ng/g. Thereinto, aac (6') -IB, blaTEM-1, ermF, qnrA, qnrD, tetG, sul1, sul2 and tetM were detected in all the analyzed samples. The absolute abundance of sul1 was the highest (5.25 × 105 copies/g-6.21 × 107 copies/g) in most of the samples. In these different habitats, the abundance of antibiotics and ARGs in river estuary was the highest, and that in reed marshes was the lowest. There was a significant positive correlation between the abundance of heavy metals (Cu, Pb, Zn, Ni, Cd, Hg) and the absolute abundance of 11 ARGs (P < 0.01). Redundancy analysis showed that Cu, Zn, intI1, TP and macrolides were the important factors affecting the distribution of ARGs. Our finding provides a more likely driving and influencing factor for the transmission of ARGs in lakes with complex and diverse habitats.
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Affiliation(s)
- Tongfei Wang
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, Hubei, China
| | - Weijun Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, Hubei, China
| | - Guiying Liao
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, Hubei, China.
| | - Meiyi Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Liqing Li
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, Hubei, China
| | - Dongsheng Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
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18
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Elbehery AHA, Beason E, Siam R. Metagenomic profiling of antibiotic resistance genes in Red Sea brine pools. Arch Microbiol 2023; 205:195. [PMID: 37061654 DOI: 10.1007/s00203-023-03531-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/19/2023] [Accepted: 03/31/2023] [Indexed: 04/17/2023]
Abstract
Antibiotic resistance (AR) is an alarming global health concern, causing an annual death rate of more than 35,000 deaths in the US. AR is a natural phenomenon, reported in several pristine environments. In this study, we report AR in pristine Red Sea deep brine pools. Antimicrobial resistance genes (ARGs) were detected for several drug classes with tetracycline and macrolide resistance being the most abundant. As expected, ARGs abundance increased in accordance with the level of human impact with pristine Red Sea samples having the lowest mean ARG level followed by estuary samples, while activated sludge samples showed a significantly higher ARG level. ARG hierarchical clustering grouped drug classes for which resistance was detected in Atlantis II Deep brine pool independent of the rest of the samples. ARG abundance was significantly lower in the Discovery Deep brine pool. A correlation between integrons and ARGs abundance in brine pristine samples could be detected, while insertion sequences and plasmids showed a correlation with ARGs abundance in human-impacted samples not seen in brine pristine samples. This suggests different roles of distinct mobile genetic elements (MGEs) in ARG distribution in pristine versus human-impacted sites. Additionally, we showed the presence of mobile antibiotic resistance genes in the Atlantis II brine pool as evidenced by the co-existence of integrases and plasmid replication proteins on the same contigs harboring predicted multidrug-resistant efflux pumps. This study addresses the role of non-pathogenic environmental bacteria as a silent reservoir for ARGs, and the possible horizontal gene transfer mechanism mediating ARG acquisition.
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Affiliation(s)
- Ali H A Elbehery
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt.
| | - Elisabeth Beason
- University of Medicine and Health Sciences, Basseterre, West Indies, Saint Kitts and Nevis
| | - Rania Siam
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, Cairo, Egypt.
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19
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Abstract
With the emergence of multidrug-resistant bacteria, infection-related death toll is on the rise. Overuse of antibiotics and their leakage into waterways have transformed the environment into a sink, resulting in bacterial resistance permeating through all tiers of the food cycle. As one of the primary sources of food, fish and fish products such as fish eggs must be studied for their ability to accumulate relevant antibiotics. While the accumulation of these pharmaceuticals has previously been studied, there remains a need to analyze these processes in real time. Electrochemical aptamer-based sensor technology allows for selective, real-time monitoring of small molecules. Herein, we report the first use of miniaturized electrochemical aptamer-based sensors for the analysis of the passive uptake of the aminoglycoside antibiotic, kanamycin, in single salmon eggs. We use pulled platinum microelectrodes and increase the surface area at the electrode tip through dendritic gold deposition. These electrodes showed a 100-fold increase in DNA immobilization on the electrode surface as compared to bare microelectrodes. Additionally, the sensors showed improved stability in complex biological media over an extended period of time when compared to the more widely used macrosensors (r = 1 mm). The sensor range was determined to extend from nanomolar to micromolar concentrations of kanamycin in fish egg lysate and when used in a single salmon egg the μ-aptasensors were able to monitor the passive uptake of kanamycin over time. The accumulation kinetics were simulated using COMSOL Multiphysics software. This research presents the first reported record of passive uptake of a small molecule in a single cell in real-time using electrochemistry.
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Affiliation(s)
- Vanshika Gupta
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
| | - Jeffrey E Dick
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
- Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47906, United States
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20
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Piksa M, Lian C, Samuel IC, Pawlik KJ, Samuel IDW, Matczyszyn K. The role of the light source in antimicrobial photodynamic therapy. Chem Soc Rev 2023; 52:1697-1722. [PMID: 36779328 DOI: 10.1039/d0cs01051k] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Antimicrobial photodynamic therapy (APDT) is a promising approach to fight the growing problem of antimicrobial resistance that threatens health care, food security and agriculture. APDT uses light to excite a light-activated chemical (photosensitiser), leading to the generation of reactive oxygen species (ROS). Many APDT studies confirm its efficacy in vitro and in vivo against bacteria, fungi, viruses and parasites. However, the development of the field is focused on exploring potential targets and developing new photosensitisers. The role of light, a crucial element for ROS production, has been neglected. What are the main parameters essential for effective photosensitiser activation? Does an optimal light radiant exposure exist? And finally, which light source is best? Many reports have described the promising antibacterial effects of APDT in vitro, however, its application in vivo, especially in clinical settings remains very limited. The restricted availability may partially be due to a lack of standard conditions or protocols, arising from the diversity of selected photosensitising agents (PS), variable testing conditions including light sources used for PS activation and methods of measuring anti-bacterial activity and their effectiveness in treating bacterial infections. We thus sought to systematically review and examine the evidence from existing studies on APDT associated with the light source used. We show how the reduction of pathogens depends on the light source applied, radiant exposure and irradiance of light used, and type of pathogen, and so critically appraise the current state of development of APDT and areas to be addressed in future studies. We anticipate that further standardisation of the experimental conditions will help the field advance, and suggest key optical and biological parameters that should be reported in all APDT studies. More in vivo and clinical studies are needed and are expected to be facilitated by advances in light sources, leading to APDT becoming a sustainable, alternative therapeutic option for bacterial and other microbial infections in the future.
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Affiliation(s)
- Marta Piksa
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Science, Weigla 12, 53-114, Wroclaw, Poland
| | - Cheng Lian
- Organic Semiconductor Centre, SUPA, School of Physics and Astronomy, University of St Andrews, Fife, KY16 9SS, UK.
| | - Imogen C Samuel
- School of Medicine, University of Manchester, Manchester, M13 9PL, UK
| | - Krzysztof J Pawlik
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Science, Weigla 12, 53-114, Wroclaw, Poland
| | - Ifor D W Samuel
- Organic Semiconductor Centre, SUPA, School of Physics and Astronomy, University of St Andrews, Fife, KY16 9SS, UK.
| | - Katarzyna Matczyszyn
- Institute of Advanced Materials, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
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21
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Cui H, Zhu D, Ding L, Wang Y, Su J, Duan G, Zhu Y. Co-occurrence of genes for antibiotic resistance and arsenic biotransformation in paddy soils. J Environ Sci (China) 2023; 125:701-711. [PMID: 36375951 DOI: 10.1016/j.jes.2022.02.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 06/16/2023]
Abstract
Paddy soils are potential hotspots of combined contamination with arsenic (As) and antibiotics, which may induce co-selection of antibiotic resistance genes (ARGs) and As biotransformation genes (ABGs), resulting in dissemination of antimicrobial resistance and modification in As biogeochemical cycling. So far, little information is available for these co-selection processes and specific patterns between ABGs and ARGs in paddy soils. Here, the 16S rRNA amplicon sequencing and high-throughput quantitative PCR and network analysis were employed to investigate the dynamic response of ABGs and ARGs to As stress and manure application. The results showed that As stress increased the abundance of ARGs and mobile genetic elements (MGEs), resulting in dissemination risk of antimicrobial resistance. Manure amendment increased the abundance of ABGs, enhanced As mobilization and methylation in paddy soil, posing risk to food safety. The frequency of the co-occurrence between ABGs and ARGs, the host bacteria carrying both ARGs and ABGs were increased by As or manure treatment, and remarkably boosted in soils amended with both As and manure. Multidrug resistance genes were found to have the preference to be co-selected with ABGs, which was one of the dominant co-occurring ARGs in all treatments, and manure amendment increased the frequency of Macrolide-Lincosamide-Streptogramin B resistance (MLSB) to co-occur with ABGs. Bacillus and Clostridium of Firmicutes are the dominant host bacteria carrying both ABGs and ARGs in paddy soils. This study would extend our understanding on the co-selection between genes for antibiotics and metals, also unveil the hidden environmental effects of combined pollution.
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Affiliation(s)
- Huiling Cui
- 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 100049, China
| | - Dong Zhu
- 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 100049, China
| | - Longjun Ding
- 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 100049, China
| | - Yifei Wang
- 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 100049, China
| | - Jianqiang Su
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Guilan Duan
- 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 100049, China.
| | - Yongguan Zhu
- 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 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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22
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Busi SB, de Nies L, Pramateftaki P, Bourquin M, Kohler TJ, Ezzat L, Fodelianakis S, Michoud G, Peter H, Styllas M, Tolosano M, De Staercke V, Schön M, Galata V, Wilmes P, Battin T. Glacier-Fed Stream Biofilms Harbor Diverse Resistomes and Biosynthetic Gene Clusters. Microbiol Spectr 2023; 11:e0406922. [PMID: 36688698 PMCID: PMC9927545 DOI: 10.1128/spectrum.04069-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/22/2022] [Indexed: 01/24/2023] Open
Abstract
Antimicrobial resistance (AMR) is a universal phenomenon the origins of which lay in natural ecological interactions such as competition within niches, within and between micro- to higher-order organisms. To study these phenomena, it is crucial to examine the origins of AMR in pristine environments, i.e., limited anthropogenic influences. In this context, epilithic biofilms residing in glacier-fed streams (GFSs) are an excellent model system to study diverse, intra- and inter-domain, ecological crosstalk. We assessed the resistomes of epilithic biofilms from GFSs across the Southern Alps (New Zealand) and the Caucasus (Russia) and observed that both bacteria and eukaryotes encoded twenty-nine distinct AMR categories. Of these, beta-lactam, aminoglycoside, and multidrug resistance were both abundant and taxonomically distributed in most of the bacterial and eukaryotic phyla. AMR-encoding phyla included Bacteroidota and Proteobacteria among the bacteria, alongside Ochrophyta (algae) among the eukaryotes. Additionally, biosynthetic gene clusters (BGCs) involved in the production of antibacterial compounds were identified across all phyla in the epilithic biofilms. Furthermore, we found that several bacterial genera (Flavobacterium, Polaromonas, Superphylum Patescibacteria) encode both atimicrobial resistance genes (ARGs) and BGCs within close proximity of each other, demonstrating their capacity to simultaneously influence and compete within the microbial community. Our findings help unravel how naturally occurring BGCs and AMR contribute to the epilithic biofilms mode of life in GFSs. Additionally, we report that eukaryotes may serve as AMR reservoirs owing to their potential for encoding ARGs. Importantly, these observations may be generalizable and potentially extended to other environments that may be more or less impacted by human activity. IMPORTANCE Antimicrobial resistance is an omnipresent phenomenon in the anthropogenically influenced ecosystems. However, its role in shaping microbial community dynamics in pristine environments is relatively unknown. Using metagenomics, we report the presence of antimicrobial resistance genes and their associated pathways in epilithic biofilms within glacier-fed streams. Importantly, we observe biosynthetic gene clusters associated with antimicrobial resistance in both pro- and eukaryotes in these biofilms. Understanding the role of resistance in the context of this pristine environment and complex biodiversity may shed light on previously uncharacterized mechanisms of cross-domain interactions.
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Affiliation(s)
- Susheel Bhanu Busi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laura de Nies
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paraskevi Pramateftaki
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Massimo Bourquin
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Tyler J. Kohler
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Leïla Ezzat
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Stilianos Fodelianakis
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Grégoire Michoud
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Hannes Peter
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Michail Styllas
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matteo Tolosano
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Vincent De Staercke
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Martina Schön
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Valentina Galata
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Tom Battin
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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23
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Nawaz S, Rafiq M, Pepper IL, Betancourt WQ, Shah AA, Hasan F. Prevalence and abundance of antibiotic-resistant genes in culturable bacteria inhabiting a non-polar passu glacier, karakorum mountains range, Pakistan. World J Microbiol Biotechnol 2023; 39:94. [PMID: 36754876 DOI: 10.1007/s11274-023-03532-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/20/2023] [Indexed: 02/10/2023]
Abstract
Natural pristine environments including cold habitats are thought to be the potent reservoirs of antibiotic-resistant genes and have been recurrently reported in polar glaciers' native bacteria, nevertheless, their abundance among the non-polar glaciers' inhabitant bacteria is mostly uncharted. Herein we evaluated antibiotic resistance profile, abundance of antibiotic-resistant genes plus class 1, 2, and 3 integron integrases in 65 culturable bacterial isolates retrieved from a non-polar glacier. The 16S rRNA gene sequencing analysis identified predominantly Gram-negative 43 (66.15%) and Gram-positive 22 (33.84%) isolates. Among the Gram-negative bacteria, Gammaproteobacteria were dominant (62.79%), followed by Betaproteobacteria (18.60%) and Alphaproteobacteria (9.30%), whereas Phyla Actinobacteria (50%) and Firmicutes (40.90%) were predominant among Gram-positive. The Kirby Bauer disc diffusion method evaluated significant antibiotic resistance among the isolates. PCR amplification revealed phylum Proteobacteria predominantly carrying 21 disparate antibiotic-resistant genes like; blaAmpC 6 (100%), blaVIM-1, blaSHV and blaDHA 5 (100%) each, blaOXA-1 1 (100%), blaCMY-4 4 (100%), followed by Actinobacteria 14, Firmicutes 13 and Bacteroidetes 11. Tested isolates were negative for blaKPC, qnrA, vanA, ermA, ermB, intl2, and intl3. Predominant Gram-negative isolates had higher MAR index values, compared to Gram-positive. Alignment of protein homology sequences of antibiotic-resistant genes with references revealed amino acid variations in blaNDM-1, blaOXA-1, blaSHV, mecA, aac(6)-Ib3, tetA, tetB, sul2, qnrB, gyrA, and intI1. Promising antibiotic-resistant bacteria, harbored with numerous antibiotic-resistant genes and class 1 integron integrase with some amino acid variations detected, accentuating the mandatory focus to evaluate the intricate transcriptome analysis of glaciated bacteria conferring antibiotic resistance.
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Affiliation(s)
- Sabir Nawaz
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Rafiq
- Department of Microbiology, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan.
| | - Ian L Pepper
- Water & Energy Sustainable Technology (WEST) Center, University of Arizona, 2959 W. Calle Agua Nueva, 85745, Tucson, AZ, USA
| | - Walter Q Betancourt
- Water & Energy Sustainable Technology (WEST) Center, University of Arizona, 2959 W. Calle Agua Nueva, 85745, Tucson, AZ, USA
| | - Aamer Ali Shah
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fariha Hasan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
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24
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Mao G, Ji M, Jiao N, Su J, Zhang Z, Liu K, Chen Y, Liu Y. Monsoon affects the distribution of antibiotic resistome in Tibetan glaciers. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120809. [PMID: 36470452 DOI: 10.1016/j.envpol.2022.120809] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Antibiotic-resistance gene (ARG) is a biological pollutant and is globally distributed due to increased anthropogenic activities. ARGs in the cryosphere have received increased attention due to global warming, and ARGs in glaciers are predicted to be released into downstream ecosystems during glacier melting. In this study, ARG distribution and influential factors were investigated in 85 samples from 21 Tibetan glaciers, covering snow, ice, and cryoconite habitats. The results revealed ARGs against 29 antibiotics in Tibetan glaciers, dominated by tetracycline, bacitracin, macrolide, and fluoroquinolone resistance. ARGs in snow exhibited biogeographic patterns influenced by atmospheric circulation. Specifically, monsoon-dominated glaciers exhibited a significantly higher abundance of ARGs than the westerly-dominated glaciers, which could be associated with higher antibiotic usage in the Indian subcontinent. Of the 3241 metagenome-assembled genomes obtained, 36.8% of which were identified as ARG hosts and 33.8% were multidrug-resistant. In addition, 90 ARGs were linked to mobile genetic elements (MGEs). 90.9% and 9.1% of MGEs were identified as plasmid and phage in 45 MAGs carrying both ARGs and MGEs. Our study suggests a greater risk of ARGs being released from the monsoon-dominated glaciers, which were the glaciers that melt at high rates and thus need to be carefully monitored.
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Affiliation(s)
- Guannan Mao
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mukan Ji
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou, 730000, China
| | - Nianzhi Jiao
- Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, 361005, China
| | - Jianqiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuying Chen
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China; Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou, 730000, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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25
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Wu D, Zhao J, Su Y, Yang M, Dolfing J, Graham DW, Yang K, Xie B. Explaining the resistomes in a megacity's water supply catchment: Roles of microbial assembly-dominant taxa, niched environments and pathogenic bacteria. WATER RESEARCH 2023; 228:119359. [PMID: 36423548 DOI: 10.1016/j.watres.2022.119359] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/30/2022] [Accepted: 11/12/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic resistance genes (ARGs) in drinking water sources suggest the possible presence of resistant microorganisms that jeopardize human health. However, explanations for the presence of specific ARGs in situ are largely unknown, especially how their prevalence is affected by local microbial ecology, taxa assembly and community-wide gene transfer. Here, we characterized resistomes and bacterial communities in the Taipu River catchment, which feeds a key drinking water reservoir to a global megacity, Shanghai. Overall, ARG abundances decreased significantly as the river flowed downstream towards the reservoir (P < 0.01), whereas the waterborne bacteria assembled deterministically (|βNRI| > 2.0) as a function of temperature and dissolved oxygen conditions with the assembly-dominant taxa (e.g. Ilumatobacteraceae and Cyanobiaceae) defining local resistomes (P < 0.01, Cohen's D = 4.22). Bacterial hosts of intragenomic ARGs stayed at the same level across the catchment (60 ∼ 70 genome copies per million reads). Among them, the putative resistant pathogens (e.g. Burkholderiaceae) carried mixtures of ARGs that exhibited high transmission probability (transfer counts = 126, P < 0.001), especially with the microbial assembly-dominant taxa. These putative resistant pathogens had densities ranging form 3.0 to 4.0 × 106 cell/L, which was more pronouncedly affected by resistome and microbial assembly structures than environmental factors (SEM, std-coeff β = 0.62 vs. 0.12). This work shows that microbial assembly and resistant pathogens play predominant roles in prevelance and dissemination of resistomes in receiving water, which deserves greater attention in devisng control strategies for reducing in-situ ARGs and resistant strains in a catchment.
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Affiliation(s)
- Dong Wu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guizhou 550001, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Jue Zhao
- Department of Civil and Environmental Engineering and Research Institute for Sustainable Urban Development, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Yinglong Su
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Mengjie Yang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Jan Dolfing
- Faculty Energy and Environment, Northumbria University, Newcastle upon Tyne, NE1 8QH, UK
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
| | - Kai Yang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, 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, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
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26
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Scott LC, Aubee A, Wilson MJ, Esser S, Descamps D, Lee N, Distler E, Aw TG. Leave No Trace? Ecological and anthropogenic determinants of antibiotic resistant bacteria in a recreational alpine environment. ENVIRONMENTAL RESEARCH 2023; 216:114617. [PMID: 36273598 DOI: 10.1016/j.envres.2022.114617] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/05/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic resistant bacteria (ARB) have been detected in remote environments, but the degree to which their presence is due to anthropogenic contamination remains unclear. Here, anthropogenic and ecological determinants of ARB were characterized in remote and highly visited areas of Rocky Mountain National Park in the United States. Soil and water samples were collected from 29 sites once a month for three months and measured for bacteria resistant to seven antibiotics with flow cytometry. A novel index of the likelihood of human presence (HPI) was generated for estimating human impact on ARB abundance. The HPI accounted for 44% of variation in ARB abundance in water samples (p < 0.0001) and 51% of variation in soil samples (p < 0.00001). Human presence index was illustrated as a reliable predictor of ARB abundance despite a tendency to underpredict at higher levels of human impact. Ecological determinants such as temperature, elevation, slope, and aspect were also found to be significantly associated with ARB abundance. These findings suggest that human presence drives the abundance of ARB in Rocky Mountain National Park, but ecological variables play a significant role in their presence and dispersal.
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Affiliation(s)
- Laura C Scott
- Tulane University School of Public Health and Tropical Medicine, Department of Environmental Health Sciences, New Orleans, LA, 70112, USA.
| | - Alexandra Aubee
- Tulane University School of Public Health and Tropical Medicine, Department of Environmental Health Sciences, New Orleans, LA, 70112, USA
| | - Mark J Wilson
- Tulane University School of Public Health and Tropical Medicine, Department of Environmental Health Sciences, New Orleans, LA, 70112, USA
| | - Scott Esser
- Continental Divide Research Learning Center, Rocky Mountain National Park, National Park Service, Estes Park, CO, 80517, USA
| | - Denisse Descamps
- Tulane University School of Public Health and Tropical Medicine, Department of Epidemiology, New Orleans, LA, 70112, USA
| | - Nicholas Lee
- Tulane University School of Public Health and Tropical Medicine, Department of Environmental Health Sciences, New Orleans, LA, 70112, USA
| | - Emiko Distler
- Tulane University School of Public Health and Tropical Medicine, Department of Environmental Health Sciences, New Orleans, LA, 70112, USA
| | - Tiong Gim Aw
- Tulane University School of Public Health and Tropical Medicine, Department of Environmental Health Sciences, New Orleans, LA, 70112, USA.
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27
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Delgado-Baquerizo M, Hu HW, Maestre FT, Guerra CA, Eisenhauer N, Eldridge DJ, Zhu YG, Chen QL, Trivedi P, Du S, Makhalanyane TP, Verma JP, Gozalo B, Ochoa V, Asensio S, Wang L, Zaady E, Illán JG, Siebe C, Grebenc T, Zhou X, Liu YR, Bamigboye AR, Blanco-Pastor JL, Duran J, Rodríguez A, Mamet S, Alfaro F, Abades S, Teixido AL, Peñaloza-Bojacá GF, Molina-Montenegro MA, Torres-Díaz C, Perez C, Gallardo A, García-Velázquez L, Hayes PE, Neuhauser S, He JZ. The global distribution and environmental drivers of the soil antibiotic resistome. MICROBIOME 2022; 10:219. [PMID: 36503688 PMCID: PMC9743735 DOI: 10.1186/s40168-022-01405-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 10/31/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth's largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs. RESULTS We show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs. CONCLUSIONS Together, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome. Video Abstract.
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Affiliation(s)
- Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain.
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, 41013, Sevilla, Spain.
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Science, Fujian Normal University, Fuzhou, 350007, China.
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
- Departamento de Ecología, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
| | - Carlos A Guerra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- Institute of Biology, Martin-Luther University Halle Wittenberg, Am Kirchtor 1, 06108, Halle (Saale), Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qing-Lin Chen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Shuai Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Thulani P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0028, South Africa
| | - Jay Prakash Verma
- Plant-Microbe Interactions Lab., Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
- Soil Microbiology Lab., Department of Soil Science, Federal University of Ceara, Fortaleza, Brazil
| | - Beatriz Gozalo
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
| | - Victoria Ochoa
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
| | - Sergio Asensio
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
| | - Ling Wang
- Institute of Grassland Science/School of Life Science, Northeast Normal University, and Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, Jilin, China
| | - Eli Zaady
- Agricultural Research Organization, Department of Natural Resources, Institute of Plant Sciences, Gilat Research Center, Mobile Post, 8531100, Negev, Israel
| | - Javier G Illán
- Department of Entomology, Washington State University, Pullman, WA, 99164, USA
| | - Christina Siebe
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, México City D.F., CP, 04510, México
| | - Tine Grebenc
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Xiaobing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, CAS, Urumqi, China
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - José L Blanco-Pastor
- INRAE, UR4 (URP3F), Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
- Department of Plant Biology and Ecology, University of Seville, Avda. Reina Mercedes 6, ES-41012, Seville, Spain
| | - Jorge Duran
- Misión Biolóxica de Galicia, Consejo Superior de Investigaciones Científicas, 36143, Pontevedra, Spain
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Alexandra Rodríguez
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Steven Mamet
- College of Agriculture and Bioresources Department of Soil Science, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Fernando Alfaro
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
| | - Sebastian Abades
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
| | - Alberto L Teixido
- Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Av. Fernando Corrêa, 2367, Boa Esperança, Cuiabá, MT, 78060-900, Brazil
| | - Gabriel F Peñaloza-Bojacá
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | | | - Cristian Torres-Díaz
- Grupo de Biodiversidad y Cambio Global (BCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Campus Fernando May, Chillán, Chile
| | - Cecilia Perez
- Instituto de Ecología y Biodiversidad, Las Palmeras 3425, Santiago, Chile
| | - Antonio Gallardo
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, 41013, Sevilla, Spain
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Laura García-Velázquez
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Patrick E Hayes
- School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Sigrid Neuhauser
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Science, Fujian Normal University, Fuzhou, 350007, China.
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Zhang Y, Zhang B, Ahmed I, Zhang H, He Y. Profiles and natural drivers of antibiotic resistome in multiple environmental media in penguin-colonized area in Antarctica. FUNDAMENTAL RESEARCH 2022. [DOI: 10.1016/j.fmre.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Li H, Luo Q, Zhao S, Zhao P, Yang X, Huang Q, Su J. Watershed urbanization enhances the enrichment of pathogenic bacteria and antibiotic resistance genes on microplastics in the water environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 313:120185. [PMID: 36108884 DOI: 10.1016/j.envpol.2022.120185] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Microplastics (MPs) serve as vectors for microorganisms and antibiotic resistance genes (ARGs) and contribute to the spread of pathogenic bacteria and ARGs across various environments. Patterns of microbial communities and ARGs in the biofilm on the surface of MPs, also termed as plastisphere, have become an issue of global concern. Although antibiotic resistome in the plastisphere has been detected, how watershed urbanization affects patterns of potential pathogens and ARGs in the microplastic biofilms is still unclear. Here, we compared the bacterial communities, the interaction between bacterial taxa, pathogenic bacteria, and ARGs between the plastisphere and their surrounding water, and revealed the extensive influence of urbanization on them. Our results showed that bacterial communities and interactions in the plastisphere differed from those in their surrounding water. Microplastics selectively enriched Bacteroidetes from water. In non-urbanized area, the abundance of Oxyphotobacteria was significantly (p < 0.05) higher in plastisphere than that in water, while α-Proteobacteria was significantly (p < 0.05) higher in plastisphere than those in water of urbanized area. Pathogenic bacteria, ARGs, and mobile genetic elements (MGEs) were significantly (p < 0.05) higher in the urbanized area than those in non-urbanized area. MPs selectively enriched ARG-carrying potential pathogens, i.e., Klebsiella pneumoniae and Enterobacter cloacae, and exhibited a distinct effect on the relative abundance of ARG and pathogens in water with different urbanization levels. We further found ARGs were significantly correlated to MGEs and pathogenic bacteria. These results suggested that MPs would promote the dissemination of ARGs among microbes including pathogenic bacteria, and urbanization would affect the impact of MPs on microbes, pathogens, and ARGs in water. A high level of urbanization could enhance the enrichment of pathogens and ARGs by MPs in aquatic systems and increase microbial risk in aquatic environments. Our findings highlighted the necessity of controlling the spread of ARGs among pathogens and the usage of plastic products in ecosystems of urban areas.
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Affiliation(s)
- Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China.
| | - Qiuping Luo
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China; College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Sha Zhao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China
| | - Peiqiang Zhao
- School of Public Utilities, Jiangsu Urban and Rural Construction College, Changzhou, 213147, PR China
| | - Xiaoru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
| | - Qiansheng Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
| | - Jianqiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
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30
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Robins K, McCann CM, Zhou XY, Su JQ, Cooke M, Knapp CW, Graham DW. Bioavailability of potentially toxic elements influences antibiotic resistance gene and mobile genetic element abundances in urban and rural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157512. [PMID: 35872194 DOI: 10.1016/j.scitotenv.2022.157512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/08/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance genes (ARGs) that can encode resistance traits in bacteria are found across the environment. While it is often difficult to discern their origin, their prevalence and diversity depends on many factors, one of which is their exposure to potentially toxic elements (PTE, i.e., metals and metalloids) in soils. Here, we investigated how ambient ARGs and mobile genetic elements (MGEs) relate to the relative bioavailability of different PTEs (total versus exchangeable and carbonate-bound PTE) in rural and urban soils in northeast England. The average relative abundances of ARGs in rural sites varied over a 3-log range (7.24 × 10-7 to 1.0 × 10-4 genes/16S rRNA), and relative ARG abundances in urban sites varied by four orders of magnitude (1.75 × 10-6 to 2.85 × 10-2 genes/16S rRNA). While beta-lactam and aminoglycoside resistance genes dominated rural and urban sites, respectively, non-specific ARGs, also called multidrug-resistance genes, were significantly more abundant in urban sites (p < 0.05). Urban sites also had higher concentrations of total and exchangeable forms of PTE than rural sites, whereas rural sites were higher in carbonate-bound forms. Significant positive Spearman correlations between PTEs, ARGs and MGEs were apparent, especially with bioavailable PTE fractions and at urban sites. This study found significant positive correlations between ARGs and beryllium (Be), which has not previously been reported. Overall, our results show that PTE bioavailability is important in explaining the relative selection of ARGs in soil settings and must be considered in future co-selection and ARG exposure studies.
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Affiliation(s)
- Katie Robins
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Clare M McCann
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom; Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
| | - Xin-Yuan Zhou
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Science, Xiamen 361021, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Science, Xiamen 361021, China
| | - Martin Cooke
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Charles W Knapp
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow G1 1XJ, United Kingdom.
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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31
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Dreyer S, Globig A, Bachmann L, Schütz AK, Schaufler K, Homeier-Bachmann T. Longitudinal Study on Extended-Spectrum Beta-Lactamase- E. coli in Sentinel Mallard Ducks in an Important Baltic Stop-Over Site for Migratory Ducks in Germany. Microorganisms 2022; 10:1968. [PMID: 36296245 PMCID: PMC9612239 DOI: 10.3390/microorganisms10101968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 08/17/2023] Open
Abstract
Antimicrobial resistance (AMR) is a serious global health threat with extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales as the most critical ones. Studies on AMR in wild birds imply a possible dissemination function and indicate their potential role as sentinel animals. This study aimed to gain a deeper insight into the AMR burden of wild waterfowl by sampling semi-wild mallard ducks used as sentinels and to identify if AMR bacteria could be recommended to be added to the pathogens of public health risks to be screened for. In total, 376 cloacal and pooled fecal samples were collected from the sentinel plant over a period of two years. Samples were screened for ESBL-carrying E. coli and isolates found further analyzed using antimicrobial susceptibility testing and whole-genome sequencing. Over the sampling period, 4.26% (16/376) of the samples were positive for ESBL-producing E. coli. BlaCTX-M-1 and blaCTX-M-32 were the most abundant CTX-M types. Although none of the top global sequence types (ST) could be detected, poultry-derived ST115 and non-poultry-related STs were found and could be followed over time. The current study revealed low cases of ESBL-producing E. coli in semi-wild mallard ducks, which proves the suitability of sentinel surveillance for AMR detection in water-associated wildlife.
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Affiliation(s)
- Sylvia Dreyer
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, 17493 Greifswald, Germany
| | - Anja Globig
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, 17493 Greifswald, Germany
| | - Lisa Bachmann
- Faculty of Agriculture and Food Science, University of Applied Science Neubrandenburg, 17033 Neubrandenburg, Germany
| | - Anne K. Schütz
- Institute of Epidemiology, Friedrich-Loeffler-Institut, 17493 Greifswald, Germany
| | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
- Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
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32
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Li T, Li R, Cao Y, Tao C, Deng X, Ou Y, Liu H, Shen Z, Li R, Shen Q. Soil antibiotic abatement associates with the manipulation of soil microbiome via long-term fertilizer application. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129704. [PMID: 36104920 DOI: 10.1016/j.jhazmat.2022.129704] [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: 05/01/2022] [Revised: 07/20/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
The effects of different fertilization on microbial communities and resistome in agricultural soils with a history of fresh manure application remains largely unclear. Here, soil antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and microbial communities were deciphered using metagenomics approach from a long-term field experiment with different fertilizer inputs. A total of 541 ARG subtypes were identified, with Multidrug, Macrolides-Lincosamides-Streptogramins (MLS), and Bacitracin resistance genes as the most universal ARG types. The abundance of ARGs detected in manure (2.52 ARGs/16 S rRNA) treated soils was higher than chemical fertilizer (2.42 ARGs/16 S rRNA) or compost (2.37 ARGs/16 S rRNA) amended soils. The higher abundance of MGEs and the enrichment of Proteobacteria were observed in manure treated soils than in chemical fertilizer or compost amended soils. Proteobacter and Actinobacter were recognized as the main potential hosts of ARGs revealed by network analysis. Further soil pH was identified as the key driver in determining the composition of both microbial community and resistome. The present study investigated the mechanisms driving the microbial community, MGEs and ARG profiles of long-term fertilized soils with ARGs contamination, and our findings could support strategies to manage the dissemination of soil ARGs.
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Affiliation(s)
- Tingting Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Ruochen Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yifan Cao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yannan Ou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Hongjun Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
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Fung YH, Kong WP, Leung ASL, Du R, So PK, Wong WL, Leung YC, Chen YW, Wong KY. NDM-1 Zn1-binding residue His116 plays critical roles in antibiotic hydrolysis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140833. [PMID: 35944887 DOI: 10.1016/j.bbapap.2022.140833] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/28/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Bacteria expressing NDM-1 have been labeled as superbugs because it confers upon them resistance to a broad range of β-lactam antibiotics. The enzyme has a di‑zinc active centre, with the Zn2 site extensively studied. The roles of active-site Zn1 ligand residues are, however, still not fully understood. We carried out structure-function studies using the mutants, H116A, H116N, and H116Q. Zinc content analysis showed that Zn1 binding was weakened by 40 to 60% in the H116 mutants. The enzymatic-activity studies showed that the lower hydrolysis rates were mainly caused by their weaker substrate binding. The catalytic efficiency (kcat/Km) of the mutants followed the order: WT > > H116Q (decreased by 4-20 fold) > H116A (decreased by 20-700 fold) ≥ H116N (decreased by 6-800 fold). The maximum effect was observed on H116N against penicillin G, whereas ampicillin was not hydrolyzed at all. The fold-increase of Km values, which informs the weakening of substrate binding, were: H116A by 5-45 fold; H116N by 6-100 fold; H116Q by 2-10 fold. Molecular dynamics simulations suggested that the Zn1 site mutations affected the positions of Zn2 and the bridging hydroxide, by 0.8 to 1.2 Å, with the largest changes of ~1.5 Å observed on Zn2 ligand C221. A native hydrogen bond between H118 and D236 was disrupted in the H116N and H116Q mutants, which led to increased flexibility of loop 10. Consequently, residue N233 was no longer maintained at an optimal position for substrate binding. H116 connected loop 7 across Zn1 to loop 10, thereby contributed to the overall integrity. This work revealed that the H116-Zn1 interaction plays a critical role in defining the substrate-binding site. From these results, it can be inferred that inhibition strategies targeting the zinc ions may be a new direction for drug development.
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Affiliation(s)
- Yik-Hong Fung
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Wai-Po Kong
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Alan Siu Lun Leung
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Ruolan Du
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Pu-Kin So
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Wing-Leung Wong
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Yun-Chung Leung
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Yu Wai Chen
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Kwok-Yin Wong
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
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Dias D, Hipólito D, Figueiredo A, Fonseca C, Caetano T, Mendo S. Unravelling the Diversity and Abundance of the Red Fox (Vulpes vulpes) Faecal Resistome and the Phenotypic Antibiotic Susceptibility of Indicator Bacteria. Animals (Basel) 2022; 12:ani12192572. [PMID: 36230313 PMCID: PMC9558537 DOI: 10.3390/ani12192572] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/05/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Antimicrobial resistance was considered one of the major concerns of the twenty-first century by the World Health Organization in 2014. A holistic approach known as “One Health” recognizes the connections and interdependence between the health of people, domestic and wild animals, plants, and the ecosystem. The red fox is the most widespread wild canid in Europe that adapts easily and is distributed in natural environments and urban and peri-urban areas due to its increasing abundance. Foxes are reservoirs and disseminators of antibiotic resistance and zoonotic agents. They interact with watercourses, soils and livestock, and although they have no gastronomic interest, they are a game species, highlighting the potential risk of contamination between them and the hunters. Our main goal was to characterize antibiotic resistance in red foxes. Several clinically relevant antibiotic resistance genes were identified, as well as multidrug-resistant bacteria. Abstract The WHO considers that antimicrobial resistance (AMR) is among the ten greatest global public health risks of the 21st century. The expansion of human populations and anthropogenically related activities, accompanied by the fragmentation of natural habitats, has resulted in increased human–wildlife interaction. Natural ecosystems are therefore subjected to anthropogenic inputs, which affect the resistome of wild animals. Thus, urgent multisectoral action is needed to achieve the Sustainable Development Goals following the One Health approach. The present work falls within the scope of this approach and aims to characterize the AMR of the faecal microbiome of the red fox (Vulpes vulpes), an opportunistic and generalist synanthropic species whose abundance has been increasing in urban and peri-urban areas. A high number of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were screened and quantified using a high-throughput qPCR approach, and the antimicrobial susceptibility of cultivable E. coli and Enterococcus spp. were assessed interpreted with both ECOFFs and clinical breakpoints. The most abundant ARGs detected confer resistance to trimethoprim and tetracyclines, although the first were absent in one of the locations studied. Several ARGs considered to be threats to human health were identified in high relative abundances (blaTEM, ermB, aadA, tetM, tetW, tetL, drfA1 and drfA17), especially in the geographical area with greater anthropogenic influence. Although at a low percentage, resistant and multidrug-resistant (MDR) E. coli and Enterococcus spp. were isolated, including one MDR E. coli showing resistance to 12 antimicrobials from 6 different classes.
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Affiliation(s)
- Diana Dias
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Dário Hipólito
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- Department of Biology, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
| | - Ana Figueiredo
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- Department of Bioscience & CEES, University of Oslo, Blindernvn, 31, 0371 Oslo, Norway
| | - Carlos Fonseca
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- ForestWISE—Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- Correspondence: (T.C.); (S.M.)
| | - Sónia Mendo
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- Correspondence: (T.C.); (S.M.)
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35
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Robins K, Leonard AFC, Farkas K, Graham DW, Jones DL, Kasprzyk-Hordern B, Bunce JT, Grimsley JMS, Wade MJ, Zealand AM, McIntyre-Nolan S. Research needs for optimising wastewater-based epidemiology monitoring for public health protection. JOURNAL OF WATER AND HEALTH 2022; 20:1284-1313. [PMID: 36170187 DOI: 10.2166/wh.2022.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Wastewater-based epidemiology (WBE) is an unobtrusive method used to observe patterns in illicit drug use, poliovirus, and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The pandemic and need for surveillance measures have led to the rapid acceleration of WBE research and development globally. With the infrastructure available to monitor SARS-CoV-2 from wastewater in 58 countries globally, there is potential to expand targets and applications for public health protection, such as other viral pathogens, antimicrobial resistance (AMR), pharmaceutical consumption, or exposure to chemical pollutants. Some applications have been explored in academic research but are not used to inform public health decision-making. We reflect on the current knowledge of WBE for these applications and identify barriers and opportunities for expanding beyond SARS-CoV-2. This paper critically reviews the applications of WBE for public health and identifies the important research gaps for WBE to be a useful tool in public health. It considers possible uses for pathogenic viruses, AMR, and chemicals. It summarises the current evidence on the following: (1) the presence of markers in stool and urine; (2) environmental factors influencing persistence of markers in wastewater; (3) methods for sample collection and storage; (4) prospective methods for detection and quantification; (5) reducing uncertainties; and (6) further considerations for public health use.
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Affiliation(s)
- Katie Robins
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK E-mail: ; School of Engineering, Newcastle University, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Anne F C Leonard
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK E-mail: ; University of Exeter Medical School, European Centre for Environment and Human Health, University of Exeter, Cornwall TR10 9FE, UK
| | - Kata Farkas
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - David W Graham
- School of Engineering, Newcastle University, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - David L Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; SoilsWest, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA 6105, Australia
| | | | - Joshua T Bunce
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK E-mail: ; School of Engineering, Newcastle University, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Jasmine M S Grimsley
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK E-mail:
| | - Matthew J Wade
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK E-mail: ; School of Engineering, Newcastle University, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Andrew M Zealand
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK E-mail:
| | - Shannon McIntyre-Nolan
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK E-mail: ; Her Majesty's Prison and Probation Service, Ministry of Justice, London, SW1H 9AJ, UK
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Arctic Psychrotolerant Pseudomonas sp. B14-6 Exhibits Temperature-Dependent Susceptibility to Aminoglycosides. Antibiotics (Basel) 2022; 11:antibiotics11081019. [PMID: 36009888 PMCID: PMC9405152 DOI: 10.3390/antibiotics11081019] [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: 05/18/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 12/04/2022] Open
Abstract
Bacteria can evade antibiotics by acquiring resistance genes, as well as switching to a non-growing dormant state without accompanying genetic modification. Bacteria in this quiescent state are called persisters, and this non-inheritable ability to withstand multiple antibiotics is referred to as antibiotic tolerance. Although all bacteria are considered to be able to form antibiotic-tolerant persisters, the antibiotic tolerance of extremophilic bacteria is poorly understood. Previously, we identified the psychrotolerant bacterium Pseudomonas sp. B14-6 from the glacier foreland of Midtre Lovénbreen in High Arctic Svalbard. Herein, we investigated the resistance and tolerance of Pseudomonas sp. B14-6 against aminoglycosides at various temperatures. This bacterium was resistant to streptomycin and susceptible to apramycin, gentamicin, kanamycin, and tobramycin. The two putative aminoglycoside phosphotransferase genes aph1 and aph2 were the most likely contributors to streptomycin resistance. Notably, unlike the mesophilic Pseudomonas aeruginosa PA14, this cold-adapted bacterium demonstrated reduced susceptibility to all tested aminoglycosides in a temperature-dependent manner. Pseudomonas sp. B14-6 at a lower temperature formed the persister cells that shows tolerance to the 100-fold minimum inhibitory concentration (MIC) of gentamicin, as well as the partially tolerant cells that withstand 25-fold MIC gentamicin. The temperature-dependent gentamicin tolerance appears to result from reduced metabolic activity. Lastly, the partially tolerant Pseudomonas sp. B14-6 cells could slowly proliferate under the bactericidal concentrations of aminoglycosides. Our results demonstrate that Pseudomonas sp. B14-6 has a characteristic ability to form cells with a range of tolerance, which appears to be inversely proportional to its growth rate.
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Lu L, He Y, Peng C, Wen X, Ye Y, Ren D, Tang Y, Zhu D. Dispersal of antibiotic resistance genes in an agricultural influenced multi-branch river network. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154739. [PMID: 35331763 DOI: 10.1016/j.scitotenv.2022.154739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Rivers in agricultural regions serve as an important sink for livestock and poultry farm runoff, fertilizer runoff, and country living sewage, which could bring antibiotic resistance genes (ARGs) contaminations. However, the diversity and distribution of ARGs has not been well documented in the agricultural influenced river. Here, the diversity of ARGs, and their relationship with biochemical factors were determined in the surface water in an agricultural region of the Jialing River and its five rural branches. The 218 unique ARGs encoding resistance to eight major antibiotic classes have been detected using high-throughput quantitative PCR. The branches of the river had a remarkably higher abundance of ARGs than the mainstream. The aminoglycoside, beta_Lactamase, MLSB, and Multidrug resistance genes were significantly enriched in the branches compared to the mainstream. Compared with the mainstream, the ARGs profiles in the branches showed obvious higher spatial variability. Significant correlation between ARGs profiles and bacterial community structures were observed, and network analysis further showed that the ARGs were associated with their potential hosts, such as Ottowia and Novosphingobium. Redundancy discrimination analysis revealed that Cu content has a significant contribution to the increase of ARGs in the river. The microbial diversity index was negatively correlated with the abundance of the ARGs. These results provide evidence for the enrichment of ARGs in the agricultural influenced river and branches due to the joint influence of chemical and microbial variables.
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Affiliation(s)
- Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yan He
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Chao Peng
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Xingyue Wen
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yuqiu Ye
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Dong Ren
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yun Tang
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Dong Zhu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China; Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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38
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Dias D, Fonseca C, Caetano T, Mendo S. Oh, deer! How worried should we be about the diversity and abundance of the faecal resistome of red deer? THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:153831. [PMID: 35151727 DOI: 10.1016/j.scitotenv.2022.153831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
The emergence of antimicrobial resistance (AMR) is a global threat to public health. Antimicrobials are used in animal production and human medicine, which contribute to the circulation of antibiotic resistance genes (ARGs) in the environment. Wildlife can be reservoirs of pathogens and resistant bacteria. Furthermore, anthropogenic pressure can influence their resistome. This work aimed to study the AMR of the faecal microbiome of red deer, one of the most important game species in Europe. To this end, a high-throughput qPCR approach was employed to screen a high number of ARGs and the antimicrobial susceptibility of indicator bacteria was determined. Several genes that confer resistance to different classes of antibiotics were identified, with the most abundant being tetracycline ARGs. Other genes were also present that are considered current and future threats to human health, and some of these were relatively abundant. Multidrug-resistant E. coli and Enterococcus spp. were isolated, although the overall level of antibiotic resistance was low. These results highlight the pressing need to know the origin and transmission of AMR in wildlife. Thus, and considering the One Health concept, studies such as this one shows the need for surveillance programs to prevent the spread of drug-resistant strains and ARGs.
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Affiliation(s)
- Diana Dias
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Carlos Fonseca
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal; ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Sónia Mendo
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
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MDR Pumps as Crossroads of Resistance: Antibiotics and Bacteriophages. Antibiotics (Basel) 2022; 11:antibiotics11060734. [PMID: 35740141 PMCID: PMC9220107 DOI: 10.3390/antibiotics11060734] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/21/2022] [Accepted: 05/26/2022] [Indexed: 01/27/2023] Open
Abstract
At present, antibiotic resistance represents a global problem in modern medicine. In the near future, humanity may face a situation where medicine will be powerless against resistant bacteria and a post-antibiotic era will come. The development of new antibiotics is either very expensive or ineffective due to rapidly developing bacterial resistance. The need to develop alternative approaches to the treatment of bacterial infections, such as phage therapy, is beyond doubt. The cornerstone of bacterial defense against antibiotics are multidrug resistance (MDR) pumps, which are involved in antibiotic resistance, toxin export, biofilm, and persister cell formation. MDR pumps are the primary non-specific defense of bacteria against antibiotics, while drug target modification, drug inactivation, target switching, and target sequestration are the second, specific line of their defense. All bacteria have MDR pumps, and bacteriophages have evolved along with them and use the bacteria’s need for MDR pumps to bind and penetrate into bacterial cells. The study and understanding of the mechanisms of the pumps and their contribution to the overall resistance and to the sensitivity to bacteriophages will allow us to either seriously delay the onset of the post-antibiotic era or even prevent it altogether due to phage-antibiotic synergy.
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Jang J, Park J, Hwang CY, Choi J, Shin J, Kim YM, Cho KH, Kim JH, Lee YM, Lee BY. Abundance and diversity of antibiotic resistance genes and bacterial communities in the western Pacific and Southern Oceans. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153360. [PMID: 35085628 DOI: 10.1016/j.scitotenv.2022.153360] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
This study investigated the abundance and diversity of antibiotic resistance genes (ARGs) and the composition of bacterial communities along a transect covering the western Pacific Ocean (36°N) to the Southern Ocean (74°S) using the Korean icebreaker R/V Araon (total cruise distance: 14,942 km). The relative abundances of ARGs and bacteria were assessed with quantitative PCR and next generation sequencing, respectively. The absolute abundance of ARGs was 3.0 × 106 ± 1.6 × 106 copies/mL in the western Pacific Ocean, with the highest value (7.8 × 106 copies/mL) recorded at a station in the Tasman Sea (37°S). The absolute abundance of ARGs in the Southern Ocean was 1.8-fold lower than that in the western Pacific Ocean, and slightly increased (0.7-fold) toward Terra Nova Bay in Antarctica, possibly resulting from natural terrestrial sources or human activity. β-Lactam and tetracycline resistance genes were dominant in all samples (88-99%), indicating that they are likely the key ARGs in the ocean. Correlation and network analysis showed that Bdellovibrionota, Bacteroidetes, Cyanobacteria, Margulisbacteria, and Proteobacteria were positively correlated with ARGs, suggesting that these bacteria are the most likely ARG carriers. This study highlights the latitudinal profile of ARG distribution in the open ocean system and provides insights that will help in monitoring emerging pollutants on a global scale.
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Affiliation(s)
- Jiyi Jang
- Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, South Korea; Ulsan National Institute of Science and Technology, 50, UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, South Korea
| | - Jiyeon Park
- Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, South Korea.
| | - Chung Yeon Hwang
- Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jinhee Choi
- Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, South Korea
| | - Jingyeong Shin
- Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul 04763, South Korea
| | - Young Mo Kim
- Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul 04763, South Korea
| | - Kyung Hwa Cho
- Ulsan National Institute of Science and Technology, 50, UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, South Korea
| | - Jung-Hyun Kim
- Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, South Korea
| | - Yung Mi Lee
- Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, South Korea
| | - Bang Yong Lee
- Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, South Korea
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41
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Smoglica C, Angelucci S, Farooq M, Antonucci A, Marsilio F, Di Francesco CE. Microbial community and antimicrobial resistance in fecal samples from wild and domestic ruminants in Maiella National Park, Italy. One Health 2022; 15:100403. [PMID: 35647256 PMCID: PMC9136667 DOI: 10.1016/j.onehlt.2022.100403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 01/04/2023] Open
Abstract
This study aimed to provide new insights about antimicrobial resistance genes abundance and microbial communities of wild and domestic ruminants in wildlife-livestock interface. In total, 88 fecal samples were recovered from Apennine chamois, red deer, goat, cattle and sheep, and were collected in pools. The populations under study were selected based on ecological data useful to define sympatric and non-sympatric populations. Samples were screened for commonly used in farms under study or critically important antimicrobial resistance genes (aadA2, TetA, TetB, TetK, TetM, mcr-1). The microbial community composition was found to be different based on the species and land use of animals under study. Indeed, it was mostly characterized by phyla Firmicutes in bovine, Bacteroidota in chamois and Proteobacteria in red deer. Additionally, positive correlations between antibiotic resistance genes and microbial taxa (e.g., Tet genes correlated with Firmicutes and Patescibacteria) were described. Of the antimicrobials investigated, the abundance of mcr-1 gene suggests the importance of monitoring the wildlife in order to detect the emerging resistance genes contamination in environment. This study provides new data that highlight the importance of multidisciplinary and uncultured study in order to describe the spreading of antimicrobial resistance and related contamination in the environment. Multidisciplinary approach including ecological data, real time PCRs and 16S rRNA analysis Microbial communities composition of rare species as Apennine chamois Evaluation of antibiotic resistance genes abundance in feces of wild and domestic ruminants Detection of mcr-1 resistance gene relevant for Public Health
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Sharma N, Kumari R, Thakur M, Rai AK, Singh SP. Molecular dissemination of emerging antibiotic, biocide, and metal co-resistomes in the Himalayan hot springs. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 307:114569. [PMID: 35091250 DOI: 10.1016/j.jenvman.2022.114569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Growing resistance among microbial communities against antimicrobial compounds, especially antibiotics, is a significant threat to living beings. With increasing antibiotic resistance in human pathogens, it is necessary to examine the habitats having community interests. In the present study, a metagenomic approach has been employed to understand the causes, dissemination, and effects of antibiotic, metal, and biocide resistomes on the microbial ecology of three hot springs, Borong, Lingdem, and Yumthang, located at different altitudes of the Sikkim Himalaya. The taxonomic assessment of these hot springs depicted the predominance of mesophilic organisms, mainly belonging to the phylum Proteobacteria. The enriched microbial metabolism assosiated with energy, cellular processes, adaptation to diverse environments, and defence were deciphered in the metagenomes. The genes representing resistance to semisynthetic antibiotics, e.g., aminoglycosides, fluoroquinolones, fosfomycin, vancomycin, trimethoprim, tetracycline, streptomycin, beta-lactams, multidrug resistance, and biocides such as triclosan, hydrogen peroxide, acriflavin, were abundantly present. Various genes attributing resistance to copper, arsenic, iron, and mercury in metal resistome were detected. Relative abundance, correlation, and genome mapping of metagenome-assembled genomes indicated the co-evolution of antibiotic and metal resistance in predicted novel species belonging to Vogesella, Thiobacillus, and Tepidimona genera. The metagenomic findings were further validated with isolation of microbial cultures, exhibiting resistance against antibiotics and heavy metals, from the hot spring water samples. The study furthers our understanding about the molecular basis of co-resistomes in the ceological niches and their possible impact on the environment.
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Affiliation(s)
- Nitish Sharma
- Center of Innovative and Applied Bioprocessing, SAS Nagar, Mohali, India; Department of Biotechnology, Panjab University, Chandigarh, India
| | - Reena Kumari
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India
| | - Monika Thakur
- Center of Innovative and Applied Bioprocessing, SAS Nagar, Mohali, India; Department of Biotechnology, Panjab University, Chandigarh, India
| | - Amit K Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India.
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, SAS Nagar, Mohali, India.
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43
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Akhil Prakash E, Hromádková T, Jabir T, Vipindas PV, Krishnan KP, Mohamed Hatha AA, Briedis M. Dissemination of multidrug resistant bacteria to the polar environment - Role of the longest migratory bird Arctic tern (Sterna paradisaea). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152727. [PMID: 34974001 DOI: 10.1016/j.scitotenv.2021.152727] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
The ever-increasing prevalence of antibiotic-resistant bacteria(ARB), primarily due to the frequent use and misuse of antibiotics, is an issue of serious global concern. Migratory birds have a significant role in dissemination of ARB, as they acquire resistant bacteria from reservoirs and transport them to other environments which are relatively less influenced by anthropogenically. We have investigated the prevalence of ARB in a long-distance migratory bird, the Arctic tern (Sterna paradisaea) captured from the Svalbard Archipelago. The birds were tagged with geolocators to track their extraordinary long migration, and the cloacal samples were collected before the migration and after the migration by recapturing the same birds. The tracking of 12 birds revealed that during the annual cycle they underwent a total of 166 stopovers (11-18, mean = 3.8) and recovery points along the Atlantic Ocean. Twelve major bacterial genera were identified from Arctic tern cloacal samples, which are dominated by Staphylococcus spp. and Aerococcus spp. The bacterial isolates showed resistance against 16 antibiotics (before migration) and 17 antibiotics (after migration) out of 17 antibiotics tested. Resistance to β-lactam and quinolone class of antibiotics were frequent among the bacteria. The study highlights the potential role of Arctic tern in the dissemination of multidrug resistant bacteria across far and wide destinations, especially to the polar environments.
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Affiliation(s)
- E Akhil Prakash
- Department of Marine Biology, Microbiology, and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682 016, India.
| | - Tereza Hromádková
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic; Centre for Polar Ecology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - T Jabir
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa 403 804, India.
| | - P V Vipindas
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa 403 804, India
| | - K P Krishnan
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa 403 804, India; CUSAT-NCPOR Centre for Polar Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682 016, India
| | - A A Mohamed Hatha
- Department of Marine Biology, Microbiology, and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682 016, India; CUSAT-NCPOR Centre for Polar Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682 016, India.
| | - Martins Briedis
- Department of Bird Migration, Swiss Ornithological Institute, 6204 Sempach, Switzerland; Lab of Ornithology, Institute of Biology, University of Latvia, 1004 Riga, Latvia
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Li H, Luo QP, Pu Q, Yang XR, An XL, Zhu D, Su JQ. Earthworms reduce the dissemination potential of antibiotic resistance genes by changing bacterial co-occurrence patterns in soil. JOURNAL OF HAZARDOUS MATERIALS 2022; 426:128127. [PMID: 34953254 DOI: 10.1016/j.jhazmat.2021.128127] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Globally distributed earthworms affect compositions of soil compounds, microbial community structures, as well as antibiotic resistance genes (ARGs). Compared to their surroundings, earthworm gut is a simpler environment which could filter out microbes when soil passes through it. However, little is known about how earthworms affect the dissemination of ARGs in soil, and the understanding of the relationship between microbe-microbe interactions and ARGs is still lacking. Here, we designed a microcosm experiment with earthworm addition, and determined bacterial and fungal community compositions based on amplicon sequencing. We also examined mobile genetic elements (MGEs) and ARGs in earthworm gut and soils using high-throughput qPCR. The results showed significant differences of bacterial, fungal and ARG patterns between gut and soil. Earthworms indirectly impacted the patterns of ARGs in soils by affecting bacterial communities and soil properties, which play key roles in the distribution of ARGs and MGEs. The absolute abundances of MGEs in earthworm gut were significantly lower than those in soils, and earthworms reduce the absolute abundance of MGEs in soils. Earthworms changed the microbial co-occurrence patterns, and reduced bacterial connectivity, which were significantly and positively correlated with MGE abundance. These results highlight the importance of earthworm on the distribution and dissemination of ARGs in soils.
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Affiliation(s)
- Hu Li
- Key Lab 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
| | - Qiu-Ping Luo
- Key Lab 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; College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiang Pu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Xiao-Ru Yang
- Key Lab 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
| | - Xin-Li An
- Key Lab 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
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jian-Qiang Su
- Key Lab 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.
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45
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Marcoleta AE, Arros P, Varas MA, Costa J, Rojas-Salgado J, Berríos-Pastén C, Tapia-Fuentes S, Silva D, Fierro J, Canales N, Chávez FP, Gaete A, González M, Allende ML, Lagos R. The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152003. [PMID: 34856283 DOI: 10.1016/j.scitotenv.2021.152003] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
The rise of multiresistant bacterial pathogens is currently one of the most critical threats to global health, encouraging a better understanding of the evolution and spread of antimicrobial resistance. In this regard, the role of the environment as a source of resistance mechanisms remains poorly understood. Moreover, we still know a minimal part of the microbial diversity and resistome present in remote and extreme environments, hosting microbes that evolved to resist harsh conditions and thus a potentially rich source of novel resistance genes. This work demonstrated that the Antarctic Peninsula soils host a remarkable microbial diversity and a widespread presence of autochthonous antibiotic-resistant bacteria and resistance genes. We observed resistance to a wide array of antibiotics among isolates, including Pseudomonas resisting ten or more different compounds, with an overall increased resistance in bacteria from non-intervened areas. In addition, genome analysis of selected isolates showed several genes encoding efflux pumps, as well as a lack of known resistance genes for some of the resisted antibiotics, including colistin, suggesting novel uncharacterized mechanisms. By combining metagenomic approaches based on analyzing raw reads, assembled contigs, and metagenome-assembled genomes, we found hundreds of widely distributed genes potentially conferring resistance to different antibiotics (including an outstanding variety of inactivation enzymes), metals, and biocides, hosted mainly by Polaromonas, Pseudomonas, Streptomyces, Variovorax, and Burkholderia. Furthermore, a proportion of these genes were found inside predicted plasmids and other mobile elements, including a putative OXA-like carbapenemase from Polaromonas harboring conserved key residues and predicted structural features. All this evidence indicates that the Antarctic Peninsula soil microbiota has a broad natural resistome, part of which could be transferred horizontally to pathogenic bacteria, acting as a potential source of novel resistance genes.
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Affiliation(s)
- Andrés E Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Macarena A Varas
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - José Costa
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Johanna Rojas-Salgado
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Sofía Tapia-Fuentes
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Daniel Silva
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - José Fierro
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Nicolás Canales
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile; FONDAP Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Miguel L Allende
- FONDAP Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Rosalba Lagos
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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46
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Zhang T, Li J, Wang N, Wang H, Yu L. Metagenomic analysis reveals microbiome and resistome in the seawater and sediments of Kongsfjorden (Svalbard, High Arctic). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151937. [PMID: 34838907 DOI: 10.1016/j.scitotenv.2021.151937] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/02/2021] [Accepted: 11/20/2021] [Indexed: 06/13/2023]
Abstract
Kongsfjorden in the high Arctic, a typical Arctic fjord, experienced long-time input of nutrients and pollutants from the remote and local resources, providing a platform for characterizing the diversity and distribution of antibiotic resistance genes (ARGs). However, the microbiome and antibiotic resistome in this pristine marine system have not been well documented. The present study aimed to characterize the diversity and distribution of bacterial communities and associated ARGs in seawater (12 samples) and sediments (13 samples) of Kongsfjorden via metagenomic analysis. In terms of both bacterial community compositions and ARG profiles, the seawater was significantly distinct from sediment. Only 29 ARG subtypes were detected in the Arctic seawater and sediments. Furthermore, three geochemical factors (i.e., longitude, depth, and PO43-) greatly influenced the bacterial communities in sediment samples, while longitude, depth, and latitude were crucial geochemical factors influencing the ARG profiles in sediment samples. Procrustes analysis revealed a significant correlation between bacterial community compositions and ARG profiles in seawater and sediment samples. Further analysis revealed the metagenome-assembled genomes (MAGs) with ARG subtypes. Overall, our study provides insights into the microbiome and resistome in a pristine Arctic fjord, thereby providing vital information for environmental management.
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Affiliation(s)
- Tao Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China.
| | - Jun Li
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Nengfei Wang
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, PR China
| | - Hao Wang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Liyan Yu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China.
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47
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A Comprehensive Profile of Antibiotic Resistance Genes in the Water Column of a Shallow-Sea Hydrothermal Vent Ecosystem. SUSTAINABILITY 2022. [DOI: 10.3390/su14031776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Antibiotic resistance genes (ARGs) became an emerging contaminant, and were found to accumulate in natural and man-made environments. A comprehensive understanding of the diversity and abundance of ARGs in pristine environments is critical for defining the baseline levels of environmental ARGs. However, there is limited information available on the ARG profiles of pristine environments, especially for shallow-sea hydrothermal vents ecosystems. Here, we combined 16S rRNA gene full-length amplicon sequencing and high-throughput quantitative PCR (HT-qPCR) to study the bacterial communities, and ARG abundance and diversity in the shallow-sea hydrothermal vent ecosystem of the Kueishantao Islet. The results of the 16S rRNA gene amplicon sequencing showed that several sulfur-cycling related bacterial genera, including Thiomicrorhabdus, Thioreductor, Sulfurovum, Sulfurimonas and Lebetimonas, dominated in the water column of the shallow-sea system. Temperature was the significant factor shaping the bacterial communities. The results of HT-qPCR analysis showed that the Kueishantao shallow-sea system harbored the lowest diversity (average 10 ARG subtypes) and abundance (average 1.0 × 10−3 copy per bacterial cell) of ARGs compared with other pristine (i.e., Tibet lake sediments, marine water and sediments) and anthropogenic-disturbed (i.e., drinking water reservoirs, urban ponds and wastewater treatment plants) environments. Procrustes analysis demonstrated a concordant pattern between the compositions of bacterial communities and ARGs in the shallow-sea system, while variation partition analysis revealed that the shared effects of physicochemical and bacterial communities explained >80% of the variation in the composition of ARGs. These results suggest that the vent bacterial communities and local environmental factors played an important role in shaping the distribution of the ARG profiles. Our study provides the first comprehensive overview of the background level of ARGs in a shallow-sea hydrothermal vent ecosystem.
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48
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Ramsamy Y, Mlisana KP, Amoako DG, Abia ALK, Ismail A, Allam M, Mbanga J, Singh R, Essack SY. Mobile genetic elements-mediated Enterobacterales-associated carbapenemase antibiotic resistance genes propagation between the environment and humans: A One Health South African study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150641. [PMID: 34606866 DOI: 10.1016/j.scitotenv.2021.150641] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
We, (1) studied carbapenem-resistant Enterobacterales (CRE) in the environment, humans, and animals, within the same geographical area and, (2) delineated the isolates' resistome, mobilome, virulome, and phylogeny. Following ethical approval, 587 samples (humans = 230, pigs = 345, and water = 12) were collected and cultured on CRE selective media. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK 2 automated platform. The resistomes, virulomes, mobilomes, and phylogenies were ascertained by whole genome sequencing. Nineteen (3.2%), i.e., 15/19 humans and 4/19 environmental, but no pig, CRE were obtained. CREs included Klebsiella pneumoniae 9/19 (47%), Enterobacter hormaechei 6/19 (32%), Klebsiella quasipneumoniae 2/19 (11%), a novel ST498 Citrobacter freundii 1/19 (5%) and Serratia marcescens 1/19 (5%). Eleven isolates were extensively drug-resistant; eight were multidrug-resistant. Sixteen CRE harbored the blaOXA-181, blaOXA-48, blaOXA-484, blaNDM-1, and blaGES-5 genes. Multiple species/clones carried blaOXA-48 and blaNDM-1 carbapenemase-encoding genes with respective mobile genetic elements (MGEs). The IncFIB(K) plasmid replicon was found in most human K. pneumoniae strains (7/9) and all environmental K. quasipneumoniae isolates; most K. pneumoniae produced OXA-181 (5/9). The (Col440I) plasmid replicon, identified in 11 (26.82%) isolates, mainly E. hormaechei (n = 6), predominated both sectors. Most β-lactamase-encoding genes were associated with class 1 integrons IntI1, insertion sequences (IS) (IS91, IS5075, IS30, IS3000, IS3, IS19, ISKpn19, IS5075) and transposons (Tn3). The IncL/M(pMU407) and IncL/M(pOXA48) plasmid replicons were found exclusively in K. pneumoniae; all but one of these strains produced OXA-181. Also, the Klebsiella spp. harbored 80 virulence genes. Phylogenomic clustered identified isolates with other carbapenemase-producing K. pneumoniae, E. hormaechei, S. marcescens, and C. freundii from different South African sources (animals, environment, and humans). We delineated the resistome, mobilome, virulome, and phylogeny of carbapenemase-producing Enterobacterales in humans and environment, highlighting antibiotic resistance genes propagation via MGEs across sectors, emphasizing a One Health approach to AMR.
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Affiliation(s)
- Yogandree Ramsamy
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Medical Microbiology, National Health Laboratory Services, Durban, South Africa; Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Koleka P Mlisana
- Medical Microbiology, National Health Laboratory Services, Durban, South Africa
| | - Daniel G Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Joshua Mbanga
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Ravesh Singh
- Medical Microbiology, National Health Laboratory Services, Durban, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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49
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Wang H, Su X, Su J, Zhu Y, Ding K. Profiling the antibiotic resistome in soils between pristine and human-affected sites on the Tibetan Plateau. J Environ Sci (China) 2022; 111:442-451. [PMID: 34949372 DOI: 10.1016/j.jes.2021.04.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 06/14/2023]
Abstract
With increasing pressure from anthropogenic activity in pristine environments, the comprehensive profiling of antibiotic resistance genes (ARGs) is essential to evaluate the potential risks from human-induced antibiotic resistance in these under-studied places. Here, we characterized the microbial resistome in relatively pristine soil samples collected from four distinct habitats on the Tibetan Plateau, using a Smart chip based high-throughput qPCR approach. We compared these to soils from the same habitats that had been subjected to various anthropogenic activities, including residential sewage discharge, animal farming, atmospheric deposition, and tourism activity. Compared to pristine samples, an average of 23.7% more ARGs were detected in the human-affected soils, and the ARGs enriched in these soils mainly encoded resistances to aminoglycoside and beta-lactam. Of the four habitats studied, soils subjected to animal farming showed the highest risks of ARG enrichment and dissemination. As shown, the number of ARGs enriched (a total of 42), their fold changes (17.6 fold on average), and the co-occurrence complexity between ARGs and mobile genetic elements were all the highest in fecal-polluted soils. As well as antibiotics themselves, heavy metals also influenced ARG distributional patterns in Tibetan environments. However, compared to urban areas, the Tibetan Plateau had a low potential for ARG selection and exhibited low carriage of ARGs by mobile genetic elements, even in environments impacted by humans, suggesting that these ARGs have a limited capacity to disseminate. The present study examined the effects of multiple anthropogenic activities on the soil resistomes in relatively pristine environments.
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Affiliation(s)
- Hang Wang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming 650224, China; National Plateau Wetlands Research Center, Southwest Forestry University, Kunming 650224, China
| | - Xiaoxuan Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jianqiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yongguan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Kai Ding
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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50
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Wang X, Han C, Lan B, Wang C, Zhu G. Antibiotic resistance genes on the Qinghai-Tibet Plateau above an elevation of 5,000 m. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:4508-4518. [PMID: 34414535 DOI: 10.1007/s11356-021-16007-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic resistance genes (ARGs) widely occur in both anthropogenic and remote environments. Several studies have investigated the distribution of antibiotic resistance in natural environments. However, the occurrence and diversity of ARGs in remote environments at high elevations have not yet been well elucidated. Abundance, diversity, as well as influencing factors of ARGs in different ecosystems on the Qinghai-Tibet Plateau beyond elevation 5,000 m were explored, using high-throughput quantitative PCR. Totally, 197 ARGs and 12 mobile genetic elements (MGEs) were determined with abundances ranging from 3.75 × 106 to 2.39 × 107 and from 2.21 × 104 to 1.62 × 106 copies g-1, respectively. Both the absolute and relative abundances of ARGs in farmland were lower than those in wetland and grassland. The diversity and dominant resistance mechanism of ARG profiles showed obvious differences among these ecosystems. Bacterial communities and MGEs significantly correlated with ARG profiles, while physico-chemical factors showed little impact. The high abundance and strong positive correlation between integron intI-1 and ARGs suggested a high potential horizontal ARG transfer. Based on the results, the Qinghai-Tibet Plateau can be regarded as a considerable ARG gene pool. This study provides insights into the provenance of ARGs at high elevations.
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Affiliation(s)
- Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chang Han
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Bangrui Lan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Wang
- South China Sea Institution, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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