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Wu H, Xu G, Yang R, Dai J, Al-Dhabi NA, Wang G, Zhou L, Tang W. Responses of soil antibiotic resistance genes to the decrease in grain size of sediment discharged into Dongting Lake, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 953:176091. [PMID: 39244058 DOI: 10.1016/j.scitotenv.2024.176091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/26/2024] [Accepted: 09/04/2024] [Indexed: 09/09/2024]
Abstract
Sediment or soil in wetlands is regarded as an important sink of antibiotic resistance genes (ARGs). However, there are no studies on the effects of sediment changes (which caused changes in soil texture) on soil ARGs in wetland. Here, we collected topsoil samples from 12 study sites that were deposited in early (prior to the 1970s) or recent years to reveal the responses of soil ARGs to the decrease in grain size of sediment discharged into Dongting Lake. The results indicated that it caused significant increases in clay content, soil organic matter (SOM), moisture, and bacterial abundance. The absolute abundance of 38 % ARG subtypes, 62 % ARG types, and the total ARG concentrations showed a significant increase. The composition of ARG profiles also showed significant changes. For mobile genetic elements (MGEs), the levels of plasmid, insertional, and transposase were significantly elevated. Notably, clay content, moisture, SOM, and bacterial abundance presented very strong positive correlation with most ARG and total ARG abundance. The contributions of physicochemical characteristics and bacterial abundance to ARG variations were ranked as follows: 16S rRNA > SOM > moisture > pH > soil texture (clay, sand and silt) > nitrate nitrogen > ammonium nitrogen. Bacterial abundance, SOM, moisture, and soil texture were the primary environmental parameters contributing to the soil ARG variations in this research. These changes of ARGs may pose risks to ecosystems and public health.
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Affiliation(s)
- Haipeng Wu
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410114, China; Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha 410114, China.
| | - Guxiang Xu
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410114, China; Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha 410114, China
| | - Ruiqing Yang
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410114, China; Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha 410114, China
| | - Juan Dai
- Changjiang River Scientific Research Institute, Wuhan 430072, China
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Guiqiao Wang
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410114, China; Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha 410114, China
| | - Lu Zhou
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410114, China; Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha 410114, China
| | - Wangwang Tang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
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Ding J, Yang W, Liu X, Zhao J, Fu X, Zhang F, Liu H. Hydraulic conditions control the abundance of antibiotic resistance genes and their potential host microorganisms in a frequently regulated river-lake system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174143. [PMID: 38908594 DOI: 10.1016/j.scitotenv.2024.174143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 06/24/2024]
Abstract
Antibiotic resistance genes (ARGs) are a growing problem that is widespread in river-lake ecosystems, where they pose a threat to the aquatic environment's health and public safety. These systems serve as critical nodes in water management, as they facilitate the equitable allocation of water resources through long-term and frequent water diversions. However, hydrological disturbances associated with water-regulation practices can influence the dynamics of their potential host microorganisms and associated resistance genes. Consequently, identifying the key ARGs and their resistance mechanisms in heavily regulated waters is vital for safeguarding human health and that of river-lake ecosystems. In this study, we examined the impact of water-regulation factors on ARGs and their hosts within a river-lake continuum using 16S rRNA and metagenomic sequencing. We found that a significant increase in ARG abundance during regulation periods (p < 0.05), especially in the aquatic environment. Key resistance genes were macB, tetA, evgS, novA, and msbA, with increased efflux pinpointed as their principal resistance mechanism. Network analysis identified Flavobacteriales, Acinetobacter, Pseudomonas, Burkholderiaceae, and Erythrobacter as key potential host microorganisms, which showed increased abundance within the water column during regulation periods (p < 0.05). Flow velocity and water depth both drove the host microorganisms and critical ARGs. Our findings underscore the importance of monitoring and mitigating the antibiotic resistance risk during water transfers in river-lake systems, thereby supporting informed management and conservation strategies.
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Affiliation(s)
- Jiewei Ding
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wei Yang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Xinyu Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jiayue Zhao
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xianting Fu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Fangfei Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Haifei Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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3
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Jorquera MA, Acuña JJ, Huerta N, Bai J, Zhang L, Xiao R, Sadowsky MJ. Multiple antibiotic resistance and herbicide catabolic profiles of bacteria isolated from Lake Villarrica surface sediments (Chile). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 358:124538. [PMID: 39002747 DOI: 10.1016/j.envpol.2024.124538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
Antibiotics and herbicides are contaminants of emerging concern in aquatic environments. Lake Villarrica is a relevant freshwater body in Chile and was recently designated a 'saturated nutrient zone'. Here, we investigated the occurrence of multiple antibiotic resistance (MAR) and herbicide catabolic profiles among bacteria present in the surface sediments of Lake Villarrica. The occurrence of antibiotic-resistant genes (ARGs; blaTEM, catA and tetM) and herbicide-catabolic genes (HCGs; phnJ and atzA) was investigated by qPCR. Subsequently, the presence of culturable bacteria with multiple resistance to amoxicillin (AMX), chloramphenicol (CHL) and oxytetracycline (OXT) was studied. Forty-six culturable MAR (AMX + CHL + OXT) strains were isolated and characterized with respect to their resistance to 11 antibiotics by using a disc diffusion assay and testing their ability to use herbicides as a nutrient source. qPCR analyses revealed that ARGs and HCGs were present in all sediment samples (101 to 103 gene copies g-1), with significant (P ≤ 0.05) higher values in sites near Villarrica city and cattle pastures. The plate method was used to recover MAR isolates from sediment (103-106 CFU g-1), and most of the 46 isolates also showed resistance to oxacillin (100%), cefotaxime (83%), erythromycin (96%) and vancomycin (93%). Additionally, 54 and 57% of the MAR isolates were able to grow on agar supplemented (50 mg L-1) with atrazine and glyphosate as nutrient sources, respectively. Most of the MAR isolates were taxonomically close to Pseudomonas (76.1%) and Pantoea (17.4%), particularly those isolated from urbanized sites (Pucón city). This study shows the presence of MAR bacteria with herbicide catabolic activity in sediments, which is valuable for conservation strategies and risk assessments of Lake Villarrica. However, major integrative studies on sediments as reservoirs or on the fate of MAR strains and traces of antibiotics and herbicides as a result of anthropic pressure are still needed.
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Affiliation(s)
- Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile; Millennium Institute Center for Genome Regulation (MI-CGR), Valenzuela Puelma 10207, La Reina, 7800003, Chile
| | - Nicole Huerta
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Junhong Bai
- School of Environment, Beijing Normal University, 19, Xinjiekouwaida Street, Haidian District, Beijing, 100875, China
| | - Ling Zhang
- School of Environment, Beijing Normal University, 19, Xinjiekouwaida Street, Haidian District, Beijing, 100875, China
| | - Rong Xiao
- College of Environment & Safety Engineering, FuZhou University, Fuzhou, China
| | - Michael J Sadowsky
- College of Agriculture, Food, and Environmental Sciences, University of Minnesota, St. Paul, Minnesota, 55108, USA
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4
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Zhou Z, Zhu R, Song Y, Zhang W, Sun B, Zhang Z, Yao H. Penguin-Driven Dissemination and High Enrichment of Antibiotic Resistance Genes in Lake Sediments across Antarctica. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 39083437 DOI: 10.1021/acs.est.4c02732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Numerous penguins can propagate pathogens with antibiotic resistance genes (ARGs) into Antarctica. However, the effects of penguin dissemination on the lake ARGs still have received little attention via guano deposition. Here, we have profiled ARGs in ornithogenic sediments subject to penguin guano (OLS) and nonornithogenic sediments (NOLS) from 16 lakes across Antarctica. A total of 191 ARGs were detected in all sediment samples, with a much higher abundance and diversity in OLS than in NOLS. Surprisingly, highly diverse and abundant ARGs were found in the OLS with a detection frequency of >40% and an absolute abundance of (2.34 × 109)-(4.98 × 109) copies g-1, comparable to those in coastal estuarine sediments and pig farms. The strong correlations of identified resistance genes with penguin guano input amount, environmental factors, mobile genetic elements, and bacterial community, in conjunction with network and redundancy analyses, all indicated that penguins were responsible for the dissemination and high enrichment of ARGs in lake sediments via the guano deposition, which might greatly outweigh local human-activity effects. Our results revealed that ARGs could be carried into lakes across the Antarctica through penguin migration, food chains, and guano deposition, which were closely connected with the widespread pollution of ARGs at the global scale.
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Affiliation(s)
- Zeming Zhou
- Institute of Polar Environment & Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Renbin Zhu
- Institute of Polar Environment & Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Yixin Song
- Institute of Polar Environment & Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Wanying Zhang
- Institute of Polar Environment & Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Bowen Sun
- Institute of Polar Environment & Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Zulin Zhang
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, U.K
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
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5
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Liu Y, Chu K, Hua Z, Li Q, Lu Y, Ye F, Dong Y, Li X. Dynamics of antibiotic resistance genes in the sediments of a water-diversion lake and its human exposure risk behaviour. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172563. [PMID: 38641096 DOI: 10.1016/j.scitotenv.2024.172563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
The dynamics and exposure risk behaviours of antibiotic resistance genes (ARGs) in the sediments of water-diversion lakes remain poorly understood. In this study, spatiotemporal investigations of ARG profiles in sediments targeting non-water (NWDP) and water diversion periods (WDP) were conducted in Luoma Lake, a typical water-diversion lake, and an innovative dynamics-based risk assessment framework was constructed to evaluate ARG exposure risks to local residents. ARGs in sediments were significantly more abundant in the WDP than in the NWDP, but there was no significant variation in their spatial distribution in either period. Moreover, the pattern of ARG dissemination in sediments was unchanged between the WDP and NWDP, with horizontal gene transfer (HGT) and vertical gene transfer (VGT) contributing to ARG dissemination in both periods. However, water diversion altered the pattern in lake water, with HGT and VGT in the NWDP but only HGT in the WDP, which were critical pathways for the dissemination of ARGs. The significantly lower ARG sediment-water partition coefficient in the WDP indicated that water diversion could shift the fate of ARGs and facilitate their aqueous partitioning. Risk assessment showed that all age groups faced a higher human exposure risk of ARGs (HERA) in the WDP than in the NWDP, with the 45-59 age group having the highest risk. Furthermore, HERA increased overall with the bacterial carrying capacity in the local environment and peaked when the carrying capacity reached three (NWDP) or four (WDP) orders of magnitude higher than the observed bacterial population. HGT and VGT promoted, whereas ODF covering gene mutation and loss mainly reduced HERA in the lake. As the carrying capacity increased, the relative contribution of ODF to HERA remained relatively stable, whereas the dominant mechanism of HERA development shifted from HGT to VGT.
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Affiliation(s)
- Yuanyuan Liu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Kejian Chu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China.
| | - Zulin Hua
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Qiming Li
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Ying Lu
- Institute for Smart City of Chongqing University in Liyang, Liyang 213300, PR China
| | - Fuzhu Ye
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Yueyang Dong
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Xiaoqing Li
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
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6
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Abbas A, Barkhouse A, Hackenberger D, Wright GD. Antibiotic resistance: A key microbial survival mechanism that threatens public health. Cell Host Microbe 2024; 32:837-851. [PMID: 38870900 DOI: 10.1016/j.chom.2024.05.015] [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: 03/18/2024] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
Antibiotic resistance (AMR) is a global public health threat, challenging the effectiveness of antibiotics in combating bacterial infections. AMR also represents one of the most crucial survival traits evolved by bacteria. Antibiotics emerged hundreds of millions of years ago as advantageous secondary metabolites produced by microbes. Consequently, AMR is equally ancient and hardwired into the genetic fabric of bacteria. Human use of antibiotics for disease treatment has created selection pressure that spurs the evolution of new resistance mechanisms and the mobilization of existing ones through bacterial populations in the environment, animals, and humans. This integrated web of resistance elements is genetically complex and mechanistically diverse. Addressing this mode of bacterial survival requires innovation and investment to ensure continued use of antibiotics in the future. Strategies ranging from developing new therapies to applying artificial intelligence in monitoring AMR and discovering new drugs are being applied to manage the growing AMR crisis.
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Affiliation(s)
- Amna Abbas
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Alexandra Barkhouse
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Dirk Hackenberger
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Gerard D Wright
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
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7
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Robins K, O'Donnell G, Neumann A, Schmidt W, Hart A, Graham DW. Antimicrobial resistance in rural rivers: Comparative study of the Coquet (Northumberland) and Eden (Cumbria) River catchments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172348. [PMID: 38614353 DOI: 10.1016/j.scitotenv.2024.172348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Many studies have characterised resistomes in river microbial communities. However, few have compared resistomes in parallel rural catchments that have few point-source inputs of antimicrobial genes (ARGs) and organisms (i.e., AMR) - catchments where one can contrast more nebulous drivers of AMR in rural rivers. Here, we used quantitative microbial profiling (QMP) to compare resistomes and microbiomes in two rural river catchments in Northern England, the Coquet and Eden in Northumberland and Cumbria, respectively, with different hydrological and geographical conditions. The Eden has higher flow rates, higher annual surface runoff, and longer periods of soil saturation, whereas the Coquet is drier and has lower flowrates. QMP analysis showed the Eden contained significantly more abundant microbes associated with soil sources, animal faeces, and wastewater than the Coquet, which had microbiomes like less polluted rivers (Wilcoxon test, p < 0.01). The Eden also had greater ARG abundances and resistome diversity (Kruskal Wallis, p < 0.05), and higher levels of potentially clinically relevant ARGs. The Eden catchment had greater and flashier runoff and more extensive agricultural land use in its middle reach, which explains higher levels of AMR in the river. Hydrological and geographic factors drive AMR in rural rivers, which must be considered in environmental monitoring programmes.
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Affiliation(s)
- Katie Robins
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Greg O'Donnell
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Anke Neumann
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Wiebke Schmidt
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Alwyn Hart
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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8
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Pourrostami Niavol K, Bordoloi A, Suri R. An overview of the occurrence, impact of process parameters, and the fate of antibiotic resistance genes during anaerobic digestion processes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:41745-41774. [PMID: 38853230 PMCID: PMC11219439 DOI: 10.1007/s11356-024-33844-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
Antibiotic resistance genes (ARGs) have emerged as a significant global health threat, contributing to fatalities worldwide. Wastewater treatment plants (WWTPs) and livestock farms serve as primary reservoirs for these genes due to the limited efficacy of existing treatment methods and microbial adaptation to environmental stressors. Anaerobic digestion (AD) stands as a prevalent biological treatment for managing sewage sludge and manure in these settings. Given the agricultural utility of AD digestate as biofertilizers, understanding ARGs' fate within AD processes is essential to devise effective mitigation strategies. However, understanding the impact of various factors on ARGs occurrence, dissemination, and fate remains limited. This review article explores various AD treatment parameters and correlates to various resistance mechanisms and hotspots of ARGs in the environment. It further evaluates the dissemination and occurrence of ARGs in AD feedstocks and provides a comprehensive understanding of the fate of ARGs in AD systems. This review explores the influence of key AD parameters such as feedstock properties, pretreatments, additives, and operational strategies on ARGs. Results show that properties such as high solid content and optimum co-digestion ratios can enhance ARG removal, while the presence of heavy metals, microplastics, and antibiotics could elevate ARG abundance. Also, operational enhancements, such as employing two-stage digestion, have shown promise in improving ARG removal. However, certain pretreatment methods, like thermal hydrolysis, may exhibit a rebounding effect on ARG levels. Overall, this review systematically addresses current challenges and offers future perspectives associated with the fate of ARGs in AD systems.
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Affiliation(s)
- Kasra Pourrostami Niavol
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA, 19122, USA
| | - Achinta Bordoloi
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA, 19122, USA
| | - Rominder Suri
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA, 19122, USA.
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9
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Henriot P, Buelow E, Petit F, Ploy MC, Dagot C, Opatowski L. Modeling the impact of urban and hospital eco-exposomes on antibiotic-resistance dynamics in wastewaters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171643. [PMID: 38471588 DOI: 10.1016/j.scitotenv.2024.171643] [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: 04/21/2023] [Revised: 01/10/2024] [Accepted: 03/09/2024] [Indexed: 03/14/2024]
Abstract
The emergence and selection of antibiotic resistance is a major public health problem worldwide. The presence of antibiotic-resistant bacteria (ARBs) in natural and anthropogenic environments threatens the sustainability of efforts to reduce resistance in human and animal populations. Here, we use mathematical modeling of the selective effect of antibiotics and contaminants on the dynamics of bacterial resistance in water to analyze longitudinal spatio-temporal data collected in hospital and urban wastewater between 2012 and 2015. Samples were collected monthly during the study period at four different sites in Haute-Savoie, France: hospital and urban wastewater, before and after water treatment plants. Three different categories of exposure variables were collected simultaneously: 1) heavy metals, 2) antibiotics and 3) surfactants for a total of 13 drugs/molecules; in parallel to the normalized abundance of 88 individual genes and mobile genetic elements, mostly conferring resistance to antibiotics. A simple hypothesis-driven model describing weekly antibiotic resistance gene (ARG) dynamics was proposed to fit the available data, assuming that normalized gene abundance is proportional to antibiotic resistant bacteria (ARB) populations in water. The detected compounds were found to influence the dynamics of 17 genes found at multiple sites. While mercury and vancomycin were associated with increased ARG and affected the dynamics of 10 and 12 identified genes respectively, surfactants antagonistically affected the dynamics of three genes. The models proposed here make it possible to analyze the relationship between the persistence of resistance genes in the aquatic environment and specific compounds associated with human activities from longitudinal data. Our analysis of French data over 2012-2015 identified mercury and vancomycin as co-selectors for some ARGs.
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Affiliation(s)
- Paul Henriot
- Epidemiology and Modeling of bacterial Evasion to Antibacterials Unit (EMEA), Institut Paris, France; MESuRS Laboratory, Conservatoire National des Arts et Métiers Paris, France; Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-Infective Evasion and Pharmacoepidemiology Team, Montigny-le-Bretonneux, France.
| | - Elena Buelow
- Université Limoges, INSERM, CHU Limoges, RESINFIT, U1092 Limoges, France; Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Fabienne Petit
- UNIROUEN, UNICAEN, CNRS, M2C, Normandie Université, Rouen, France; Sorbonne Université, CNRS, EPHE, PSL, UMR METIS, Paris, France
| | - Marie-Cécile Ploy
- Université Limoges, INSERM, CHU Limoges, RESINFIT, U1092 Limoges, France
| | - Christophe Dagot
- Université Limoges, INSERM, CHU Limoges, RESINFIT, U1092 Limoges, France
| | - Lulla Opatowski
- Epidemiology and Modeling of bacterial Evasion to Antibacterials Unit (EMEA), Institut Paris, France; Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-Infective Evasion and Pharmacoepidemiology Team, Montigny-le-Bretonneux, France
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10
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Shi X, Shen Z, Shao B, Shen J, Wu Y, Wang S. Antibiotic resistance genes profile in the surface sediments of typical aquaculture areas across 15 major lakes in China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 347:123709. [PMID: 38447655 DOI: 10.1016/j.envpol.2024.123709] [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: 08/15/2023] [Revised: 02/28/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
Aquatic farming is considered as a major source of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) for the natural environment of the lakes. ARB and ARGs in the natural environment have increased quickly because of the human activities. Here, we have profiled the diversity and abundance of ARGs in sediments from the typical aquaculture areas around 15 major lakes in China using PCR and qPCR, and further assessed the risk factor shaping the occurrence and distribution of ARGs. And class 1, 2 and 3 integrons were initially detected by PCR with specific primers. ARGs were widely distributed in the lakes: Weishan Lake and Poyang Lake showed high diversity of ARGs, followed by Dongting Lake, Chao Lake and Tai Lake. Generally, the ARGs in the Middle-Lower Yangtze Plain were more abundant than those in the Qinghai-Tibet Plateau. Tetracycline resistance genes (tet(C), tet(A) & tet(M)) were prominent in sediments, and the next was AmpC β-lactamase gene group BIL/LAT/CMY, and the last was the genes resistance to aminoglycoside (strA-strB). Partial least squares path modeling analysis (PLS-PMA) revealed that livestock had a significant direct effect on the distribution of ARGs in lakes, and population might indirectly influence the profiles of ARGs by affecting the scale of livestock and aquaculture. The detectable rate of class 1, 2 and 3 integrons were 80%, 100% and 46.67%, respectively. The prevalence of integrons might play a key role in promoting more frequent horizontal gene transfer (HGT) events, resulting in the environmental mobilization and dissemination of ARGs between bacteria.
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Affiliation(s)
- Xiaomin Shi
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Zhangqi Shen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Bing Shao
- Beijing Centers for Disease Control and Preventative Medical Research, Beijing, 100013, China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Yongning Wu
- Research Unit of Food Safety (2019RU014), Chinese Academy of Medical Sciences, NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, China
| | - Shaolin Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
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11
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Kong M, Zhang Y, Ma Y, Fang H, Wang W, Shi G, Yan Y, Zhang S. Antibiotics and antibiotic resistance change bacterial community compositions in marine sediments. ENVIRONMENTAL RESEARCH 2024; 244:118005. [PMID: 38135101 DOI: 10.1016/j.envres.2023.118005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 12/24/2023]
Abstract
Emerging contaminants, including antibiotics, antibiotic-resistant bacteria (ARB), and extracellular antibiotic resistance genes (eARGs), have been detected in large numbers in the aquatic environment. The effects of emerging contaminants on bacterial communities in marine sediments are not well studied. In this study, the effects of emerging contaminants (antibiotics, ARB, and eARGs) on the variations of bacterial populations in marine sediments of the Bohai Sea, Yellow Sea, East China Sea, and South China Sea were investigated. The results showed that the abundance of the host bacterial phylum Probacteria in the marine sediments of the Bohai Sea was the lowest among the four seas after exposure to different antibiotics, ARB, and eARGs. The inputs of exogenous antibiotics and resistance genes significantly affected the community function, resulting in significant differences in community abundance at the genus level. The abundance of Halomonas, Sulfitobacter, and Alcanivorax in the four sea areas displayed noteworthy differences in response to the addition of exogenous antibiotics and eARGs. These findings contribute to a more comprehensive understanding of the intricate interplay between emerging contaminants and the dynamics of bacterial communities in natural ecosystems.
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Affiliation(s)
- Ming Kong
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China.
| | - Yu Zhang
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Yan Ma
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Hao Fang
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Wanzhong Wang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Gaoling Shi
- Key Laboratory of Agro-Environment in Downstream of Yangtze River Plain, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Yan Yan
- Centre for Ecology Environment Monitoring and Scientific research, SongLiao River Basin Ecology and Environment Adiministration, Ministry of Ecology and Environment, China
| | - Shuai Zhang
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China.
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12
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Knorr S, Weisener CG, Phillips LA. The role of agricultural drainage, storm-events, and natural filtration on the biogeochemical cycling capacity of aquatic and sediment environments in Lake Erie's drainage basin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167102. [PMID: 37717759 DOI: 10.1016/j.scitotenv.2023.167102] [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: 04/27/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
Lake Erie is the most at risk of the Great Lakes for degraded water quality due to non-point source pollution caused by agricultural activities in the lake's watershed. The extent and temporal patterns of nutrient loading from these agricultural activities is influenced by the timing of agronomic events, precipitation events, and water flow through areas of natural filtration within the watershed. Downstream impacts of these nutrient loading events may be moderated by the co-loading of functionally relevant biogeochemical cycling microbial communities from agricultural soils. This study quantified loading patterns of these communities from tile drain sources, assessed whether functional communities from agricultural sources influenced downstream microbial functionality, and investigated how distance from agricultural sources, storm events, and areas of natural filtration altered nutrient cycling and nutrient fluxes in aquatic and sediment environments. Water and sediment samples were collected in the Wigle Creek watershed in Ontario, from tile drains through to Lake Erie, from May to November 2021, and microbial nitrogen (N) and phosphorous (P) cycling capacity (quantitative PCR), and nutrient levels were evaluated. Results showed that N and P functional groups were co-loaded with nutrients, with increased loading occurring during storm events and during agricultural activities including fertilization and harvest. Overall functional capacity in the aquatic environment decreased with distance from the agricultural sources and as water transited through natural filtration areas. In contrast, the sediment environment was more resilient to both agricultural disturbances and abiotic factors. This study expands our understanding of when and where different stages of N and P cycling occurs in agriculturally impacted watersheds, and identifies both seasons and regions to target with nutrient mitigation strategies.
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Affiliation(s)
- S Knorr
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, ON N0R 1G0, Canada; Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - C G Weisener
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - L A Phillips
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, ON N0R 1G0, Canada.
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13
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Timms VJ, Hassan KA, Pearson LA, Neilan BA. Cyanobacteria as a critical reservoir of the environmental antimicrobial resistome. Environ Microbiol 2023; 25:2266-2276. [PMID: 37365851 DOI: 10.1111/1462-2920.16453] [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: 04/11/2023] [Accepted: 06/04/2023] [Indexed: 06/28/2023]
Abstract
Antimicrobial resistance (AMR) is predicted to cause a worldwide annual toll of 10 million deaths by 2050. This looming public health threat has been linked to antibiotic overuse and pollution, which places selective pressures on AMR maintenance and transfer in and between microbial populations. We examined the distribution, diversity and potential mobility of AMR genes in cyanobacteria. While cyanobacteria are not pathogenic, we hypothesised that they could be a major environmental reservoir for AMR genes. Genes encoding AMR to seven antimicrobial drug classes were found in 10% of cyanobacterial genomes. AMR genes were found in 13% of freshwater, 19% of terrestrial, 34% of symbiotic, 2% of thermal spring, and 3% of marine genomes. AMR genes were found in five cyanobacterial orders with 23% of Nostocales and 8% of Oscillatoriales strains containing AMR genes. The most frequently observed alleles were ansamycin resistance genes, which were present in 7% of strains. AMR genes responsible for resistance to broad-spectrum β-lactams, chloramphenicols, tetracyclines, macrolides, and aminoglycosides were associated with mobile genetic elements or plasmid replicons or both. These results suggest that cyanobacteria are an extensive reservoir, and potential vector, for AMR genes in diverse terrestrial and aquatic habitats.
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Affiliation(s)
- V J Timms
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - K A Hassan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - L A Pearson
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - B A Neilan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
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14
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Campos MA, Zhang Q, Acuña JJ, Rilling JI, Ruiz T, Carrazana E, Reyno C, Hollenback A, Gray K, Jaisi DP, Ogram A, Bai J, Zhang L, Xiao R, Elias M, Sadowsky MJ, Hu J, Jorquera MA. Structure and Functional Properties of Bacterial Communities in Surface Sediments of the Recently Declared Nutrient-Saturated Lake Villarrica in Southern Chile. MICROBIAL ECOLOGY 2023; 86:1513-1533. [PMID: 36752910 DOI: 10.1007/s00248-023-02173-2] [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: 05/16/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Lake Villarrica, one of Chile's main freshwater water bodies, was recently declared a nutrient-saturated lake due to increased phosphorus (P) and nitrogen (N) levels. Although a decontamination plan based on environmental parameters is being established, it does not consider microbial parameters. Here, we conducted high-throughput DNA sequencing and quantitative polymerase chain reaction (qPCR) analyses to reveal the structure and functional properties of bacterial communities in surface sediments collected from sites with contrasting anthropogenic pressures in Lake Villarrica. Alpha diversity revealed an elevated bacterial richness and diversity in the more anthropogenized sediments. The phylum Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria dominated the community. The principal coordinate analysis (PCoA) and redundancy analysis (RDA) showed significant differences in bacterial communities of sampling sites. Predicted functional analysis showed that N cycling functions (e.g., nitrification and denitrification) were significant. The microbial co-occurrence networks analysis suggested Chitinophagaceae, Caldilineaceae, Planctomycetaceae, and Phycisphaerae families as keystone taxa. Bacterial functional genes related to P (phoC, phoD, and phoX) and N (nifH and nosZ) cycling were detected in all samples by qPCR. In addition, an RDA related to N and P cycling revealed that physicochemical properties and functional genes were positively correlated with several nitrite-oxidizing, ammonia-oxidizing, and N-fixing bacterial genera. Finally, denitrifying gene (nosZ) was the most significant factor influencing the topological characteristics of co-occurrence networks and bacterial interactions. Our results represent one of a few approaches to elucidate the structure and role of bacterial communities in Chilean lake sediments, which might be helpful in conservation and decontamination plans.
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Affiliation(s)
- Marco A Campos
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Qian Zhang
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, 361100, People's Republic of China
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Joaquin I Rilling
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Tay Ruiz
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Elizabeth Carrazana
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Doctorado en Ciencias mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Cristóbal Reyno
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Doctorado en Ciencias mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Anthony Hollenback
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Katelyn Gray
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Deb P Jaisi
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Andrew Ogram
- Soil and Water Sciences Department, University of Florida, PO Box 110290, Gainesville, FL, 32608-32611, USA
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Ling Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Rong Xiao
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Mikael Elias
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
| | - Jingming Hu
- College of the Environment & Ecology, Xiamen University, Xiamen, 361100, People's Republic of China
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
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15
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Gu Y, Li Z, Lei P, Wang R, Xu H, Friman VP. Phylogenetic distance-decay patterns are not explained by local community assembly processes in freshwater lake microbial communities. Environ Microbiol 2023; 25:1940-1954. [PMID: 37254577 DOI: 10.1111/1462-2920.16437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
While water and sediment microbial communities exhibit pronounced spatio-temporal patterns in freshwater lakes, the underlying drivers are yet poorly understood. Here, we evaluated the importance of spatial and temporal variation in abiotic environmental factors for bacterial and microeukaryotic community assembly and distance-decay relationships in water and sediment niches in Hongze Lake. By sampling across the whole lake during both Autumn and Spring sampling time points, we show that only bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers. Nevertheless, consistent distance-decay relationships were found with both bacterial and microeukaryotic communities, which were relatively stable with both sampling time points. Our results suggest that spatio-temporal variation in environmental factors was important in explaining mainly bacterial community assembly in the sediment, possibly due lesser disturbance. However, clear distance-decay patterns emerged also when the community assembly was stochastic. Together, these results suggest that abiotic environmental factors do not clearly drive the spatial structuring of lake microbial communities, highlighting the need to understand the role of other potential drivers, such as spatial heterogeneity and biotic species interactions.
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Affiliation(s)
- Yian Gu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, China
| | - Zhidan Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Peng Lei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Rui Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Ville-Petri Friman
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Department of Biology, University of York, York, UK
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16
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Mao C, Li Q, Komijani M, Huang J, Li T. Metagenomic analysis reveals the dissemination mechanisms and risks of resistance genes in plateau lakes. iScience 2023; 26:107508. [PMID: 37664620 PMCID: PMC10470376 DOI: 10.1016/j.isci.2023.107508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/09/2023] [Accepted: 07/25/2023] [Indexed: 09/05/2023] Open
Abstract
Antibiotic resistance genes (ARGs) are emerging as environmental pollutants that can persist and disseminate in aquatic environments. Lakes, as important sources of freshwater, also serve as potential natural reservoirs of ARGs. In this study, we analyzed the distribution and potential risks of resistance genes in five typical freshwater lakes on the Yunnan-Guizhou Plateau. Our findings revealed that multidrug and MLS ARGs dominated in the studied lakes. Notably, while Lugu Lake exhibited higher abundance of ARGs, mobile genetic elements (MGEs), and metal resistance genes (MRGs), a greater resistome risk was observed in the eutrophic Xingyun Lake. The dissemination processes of ARGs and MRGs are primarily driven by microbial communities and the horizontal gene transfer via MGEs. Limnohabitans, Flavobacterium, and Acinetobacter were identified as key players in the dissemination of ARGs. Our study highlights the persistence of ARGs and provides valuable baseline data and risk assessment of ARGs in plateau freshwater lakes.
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Affiliation(s)
- Chengzhi Mao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Majid Komijani
- Department of Biology, Faculty of Science, Arak University, Arak, Iran
| | - Jie Huang
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Tao Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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17
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Lu Y, Wang M, Yu C, Wu Q, Mao Z, Li H, Ren L, Zeng J, Xing P, Zhou LJ, Wan S, Wu QL. Unexpected enrichment of antibiotic resistance genes and organic remediation genes in high-altitude lakes at Eastern Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 874:162554. [PMID: 36870490 DOI: 10.1016/j.scitotenv.2023.162554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/07/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
Elevation has a strong effect on aquatic microbiome. However, we know little about the effects of elevation on functional genes, especially antibiotic resistance genes (ARGs) and organic remediation genes (ORGs) in freshwater ecosystems. In this study, we analyzed five classes of functional genes including ARGs, metal resistance genes (MRGs), ORGs, bacteriophages, and virulence genes between two high-altitude lakes (HALs) and two low-altitude lakes (LALs) in Mountain Siguniang at Eastern Tibetan Plateau by means of GeoChip 5.0. No differences (Student's t-test, p > 0.05) of gene richness including ARGs, MRGs, ORGs, bacteriophages, and virulence genes in HALs and LALs were found. The abundance of most ARGs and ORGs was higher in HALs than in LALs. For MRGs, the abundance of macro metal resistance genes of potassium, calcium, and aluminum was higher in HALs than in LALs (Student's t-test, p < 0.05; all Cohen's d > 0.8). The abundance of some heavy metal resistance genes of lead and mercury was lower in HALs than in LALs (Student's t-test, p < 0.05; all Cohen's d < -0.8). The composition of these functional genes in HALs differed significantly from in LALs. The functional gene network in HALs was also more complex than that in LALs. We speculate that enrichment of ARGs and ORGs in HALs is related to different microbial communities, exogenous ARGs, and enriched persistent organic pollutants through long-range atmospheric transport driven by the Indian monsoon. This study highlights the unexpected enrichment of ARGs, MRGs, and ORGs in remote lakes at high elevations.
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Affiliation(s)
- Yiwei Lu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Man Wang
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chunyan Yu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qiong Wu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhendu Mao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Huabing Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Lijuan Ren
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Li-Jun Zhou
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Shiqiang Wan
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Qinglong L Wu
- Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
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18
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Ma D, Chen H, Feng Q, Zhang X, Wu D, Feng J, Cheng S, Wang D, Liu Z, Zhong Q, Wei J, Liu G. Dissemination of antibiotic resistance genes through fecal sewage treatment facilities to the ecosystem in rural area. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 333:117439. [PMID: 36758406 DOI: 10.1016/j.jenvman.2023.117439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Infection of antibiotic-resistant pathogens mostly occurs in rural areas. In this paper, the dissemination of antibiotic resistance genes (ARGs) through fecal sewage treatment facilities to the ecosystem in a typical rural area is investigated. Household three-chamber septic tanks (TCs), household biogas digesters (BDs), wastewater treatment plants (WWTPs), vegetable plots, water ponds, etc. Are taken into account. The relative abundance of ARGs in fecal sewage can be reduced by BDs and WWTPs by 80% and 60%, respectively. While TCs show no reduction ability for ARGs. Fast expectation-maximization microbial source tracking (FEAST) analysis revealed that TCs and BDs contribute a considerable percentage (15-22%) of ARGs to the surface water bodies (water ponds) in the rural area. Most ARGs tend to precipitate in the sediments of water bodies and stop moving downstream. Meanwhile, the immigration of microorganisms is more active than that of ARGs. The results provide scientific basic data for the management of fecal sewage and the controlling of ARGs in rural areas.
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Affiliation(s)
- Dachao Ma
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
| | - Hongcheng Chen
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
| | - Qingge Feng
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China.
| | - Xuan Zhang
- College of Civil Engineering and Architecture, Guangxi University, Nanning 530004, China
| | - Deli Wu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, People's Republic of China
| | - Jinghang Feng
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
| | - Shikun Cheng
- School of Energy and Environmental Engineering, Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing , 100083, China
| | - Dongbo Wang
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
| | - Zheng Liu
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
| | - Qisong Zhong
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
| | - Jinye Wei
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
| | - Guozi Liu
- School of Resources, Environment and Materials, Key Laboratory of Environmental Protection, Guangxi University, Nanning, 530004, China
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Li S, Wu Y, Zheng H, Li H, Zheng Y, Nan J, Ma J, Nagarajan D, Chang JS. Antibiotics degradation by advanced oxidation process (AOPs): Recent advances in ecotoxicity and antibiotic-resistance genes induction of degradation products. CHEMOSPHERE 2023; 311:136977. [PMID: 36309060 DOI: 10.1016/j.chemosphere.2022.136977] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/09/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic contamination could cause serious risks of ecotoxicity and resistance gene induction. Advanced oxidation processes (AOPs) such as Fenton, photocatalysis, activated persulfate, electrochemistry and other AOPs technologies have been proven effective in the degradation of high-risk, refractory organic pollutants such as antibiotics. However, due to the limited mineralization ability, a large number of degradation intermediates will be produced in the oxidation process. The residual or undiscovered ecological risks of degradation products are potential safety hazards and problems necessitating comprehensive studies. In-depth investigations especially on the full assessments of ecotoxicity and resistance genes induction capability of antibiotic degradation products are important issues in reducing the environmental problems of antibiotics. Therefore, this review presents an overview of the current knowledge on the efficiency of different AOPs systems in reducing antibiotics toxicity and antibiotic resistance.
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Affiliation(s)
- Shuo Li
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China; Urban Water Resources Development and Northern National Engineering Research Center, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Yanan Wu
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
| | - Heshan Zheng
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China.
| | - Hongbin Li
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
| | - Yongjie Zheng
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
| | - Jun Nan
- Urban Water Resources Development and Northern National Engineering Research Center, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Jun Ma
- Urban Water Resources Development and Northern National Engineering Research Center, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Dillirani Nagarajan
- Department of Chemical Engineering, National Cheng-Kung University, Tainan, Taiwan
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng-Kung University, Tainan, Taiwan; Department of Chemical and Materials Engineering, Tunghai University, Taichung, 407, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung, 407, Taiwan; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-Li, Taiwan.
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20
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Ogunlaja A, Ogunlaja OO, Olukanni OD, Taylor GO, Olorunnisola CG, Dougnon VT, Mousse W, Fatta-Kassinos D, Msagati TAM, Unuabonah EI. Antibiotic resistomes and their chemical residues in aquatic environments in Africa. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 312:119783. [PMID: 35863703 DOI: 10.1016/j.envpol.2022.119783] [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: 01/28/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The aquatic environment is a hotspot for the transfer of antibiotic resistance to humans and animals. Several reviews have put together research efforts on the presence and distribution of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antibiotic chemical residue (ACRs) in food, hospital wastewater, and even in other aquatic environments. However, these reports are largely focused on data from developed countries, while data from developing countries and especially those in Africa, are only marginally discussed. This review is the first effort that distills information on the presence and distribution of ARGs and ACRs in the African aquatic environments (2012-2021). This review provides critical information on efforts put into the study of ARB, ARGs, and ACRs in aquatic environments in Africa through the lens of the different sub-regions in the continent. The picture provided is compared with those from some other continents in the world. It turns out that the large economies in Africa (South Africa, Nigeria, Tunisia, Kenya) all have a few reports of ARB and ARGs in their aquatic environment while smaller economies in the continent could barely provide reports of these in their aquatic environment (in most cases no report was found) even though they have some reports on resistomes from clinical studies. Interestingly, the frequency of these reports of ARB and ARGs in aquatic environments in Africa suggests that the continent is ahead of the South American continent but behind Europe and Asia in relation to providing information on these contaminants. Common ARGs found in African aquatic environment encode resistance to sulfonamide, tetracycline, β-lactam, and macrolide classes of antibiotics. The efforts and studies from African scientists in eliminating ARB and ARGs from the aquatic environment in Africa are also highlighted. Overall, this document is a ready source of credible information for scientists, policy makers, governments, and regional bodies on ARB, ARGs, and ACRs in aquatic environments in Africa. Hopefully, the information provided in this review will inspire some necessary responses from all stakeholders in the water quality sector in Africa to put in more effort into providing more scientific evidence of the presence of ARB, ARGs, and ACRs in their aquatic environment and seek more efficient ways to handle them to curtail the spread of antibiotic resistance among the population in the continent. This will in turn, put the continent on the right path to meeting the United Nations Sustainable Development Goals #3 and #6, which at the moment, appears to be largely missed by most countries in the continent.
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Affiliation(s)
- Aemere Ogunlaja
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, P.M.B 230, Ede, 232101, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, P.M.B 230, Ede, Osun State, Nigeria.
| | - Olumuyiwa O Ogunlaja
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, P.M.B 230, Ede, 232101, Osun State, Nigeria; Department of Chemical Sciences, Faculty of Natural and Applied Sciences, Lead City University, Ibadan, Nigeria
| | - Olumide D Olukanni
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, P.M.B 230, Ede, 232101, Osun State, Nigeria; Department of Biochemistry, Faculty of Basic Medical Sciences, Redeemer's University, P.M.B. 230, Ede, Nigeria
| | - Gloria O Taylor
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, P.M.B 230, Ede, 232101, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, P.M.B 230, Ede, Osun State, Nigeria
| | - Chidinma G Olorunnisola
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, P.M.B 230, Ede, 232101, Osun State, Nigeria; Department of Chemical Sciences, Faculty of Natural Sciences, Redeemer's University, P.M.B 230, Ede, Osun State, Nigeria
| | - Victorien T Dougnon
- Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Benin
| | - Wassiyath Mousse
- Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Benin
| | - Despo Fatta-Kassinos
- Department of Civil and Environmental Engineering and Nireas-International Water Research Centre, School of Engineering, University of Cyprus, PO Box 20537, 1678 Nicosia, Cyprus
| | - Titus A M Msagati
- Institute for Nanotechnology and Water Sustainability (iNanoWS), College of Science Engineering and Technology, University of South Africa, South Africa
| | - Emmanuel I Unuabonah
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, P.M.B 230, Ede, 232101, Osun State, Nigeria; Department of Chemical Sciences, Faculty of Natural Sciences, Redeemer's University, P.M.B 230, Ede, Osun State, Nigeria
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21
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Tapia-Arreola AK, Ruiz-Garcia DA, Rodulfo H, Sharma A, De Donato M. High Frequency of Antibiotic Resistance Genes (ARGs) in the Lerma River Basin, Mexico. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192113988. [PMID: 36360888 PMCID: PMC9657182 DOI: 10.3390/ijerph192113988] [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: 09/04/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 05/31/2023]
Abstract
The spread of beta-lactamase-producing bacteria is of great concern and the environment has been found to be a main source of contamination. Herein, it was proposed to determine the frequency of antimicrobial-resistant-Gram-negative bacteria throughout the Lerma River basin using phenotypic and molecular methods. Resistant bacteria were isolated with chromogenic media and antimicrobial susceptibility tests were used to characterize their resistance. ARGs for beta-lactams, aminoglycosides, and quinolones were detected by PCR. Species were identified by Sanger sequencing the 16S rRNA gene and the representative genomes of MDR strains were sequenced by NGS. A high variation in the number of isolates was observed in the 20 sampled sites, while observing a low diversity among the resistant bacteria. Of the 12 identified bacterial groups, C. freundii, E. coli, and S. marcescens were more predominant. A high frequency of resistance to beta-lactams, quinolones, and aminoglycosides was evidenced, where the blaCTX,qnrB, qnrS y, and aac(6')lb-cr genes were the most prevalent. C. freundii showed the highest frequency of MDR strains. Whole genome sequencing revealed that S. marcescens and K. pneumoniae showed a high number of shared virulence and antimicrobial resistance genes, while E. coli showed the highest number of unique genes. The contamination of the Lerma River with MDR strains carrying various ARGs should raise awareness among environmental authorities to assess the risks and regulations regarding the optimal hygienic and sanitary conditions for this important river that supports economic activities in the different communities in Mexico.
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22
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Kraemer SA, Barbosa da Costa N, Oliva A, Huot Y, Walsh DA. A resistome survey across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use. Front Microbiol 2022; 13:995418. [PMID: 36338036 PMCID: PMC9629221 DOI: 10.3389/fmicb.2022.995418] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Our decreasing ability to fight bacterial infections is a major health concern. It is arising due to the evolution of antimicrobial resistance (AMR) in response to the mis- and overuse of antibiotics in both human and veterinary medicine. Lakes integrate watershed processes and thus may act as receptors and reservoirs of antibiotic resistance genes (ARGs) introduced into the watershed by human activities. The resistome – the diversity of ARGs – under varying anthropogenic watershed pressures has been previously studied either focused on few select genes or few lakes. Here, we link the resistome of ~350 lakes sampled across Canada to human watershed activity, trophic status, as well as point sources of ARG pollution including wastewater treatment plants and hospitals in the watershed. A high percentage of the resistance genes detected was either unimpacted by human activity or highly prevalent in pristine lakes, highlighting the role of AMR in microbial ecology in aquatic systems, as well as a pool of genes available for potential horizontal gene transfer to pathogenic species. Nonetheless, watershed agricultural and pasture area significantly impacted the resistome. Moreover, the number of hospitals and the population density in a watershed, the volume of wastewater entering the lake, as well as the fraction of manure applied in the watershed as fertilizer significantly impacted ARG diversity. Together, these findings indicate that lake resistomes are regularly stocked with resistance genes evolved in the context of both veterinary and human antibiotics use and represent reservoirs of ARGs that require further monitoring.
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Affiliation(s)
- Susanne A. Kraemer
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Department of Biology, Concordia University, Montreal, QC, Canada
- *Correspondence: Susanne A. Kraemer,
| | | | - Anais Oliva
- Department of Applied Geomatics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Yannick Huot
- Department of Applied Geomatics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - David A. Walsh
- Department of Biology, Concordia University, Montreal, QC, Canada
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23
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He J, Zhang N, Shen X, Muhammad A, Shao Y. Deciphering environmental resistome and mobilome risks on the stone monument: A reservoir of antimicrobial resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156443. [PMID: 35660621 DOI: 10.1016/j.scitotenv.2022.156443] [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: 03/28/2022] [Revised: 05/30/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Antimicrobial resistance (AMR) in the environment has attracted increasing attention as an emerging global threat to public health. Stone is an essential ecosystem in nature and also an important material for human society, having architectural and aesthetic values. However, little is known about the AMR in stone ecosystems, particularly in the stone monument, where antimicrobials are often applied against biodeterioration. Here, we provide the first detailed metagenomic study of AMR genes across different types of biodeteriorated stone monuments, which revealed abundant and diverse AMR genes conferring resistance to drugs (antibiotics), biocides, and metals. Totally, 132 AMR subtypes belonging to 27 AMR types were detected including copper-, rifampin-, and aminocoumarins-resistance genes, of which diversity was mainly explained by the spatial turnover (replacement of genes between samples) rather than nestedness (loss of nested genes between samples). Source track analysis confirms that stone resistomes are likely driven by anthropogenic activities across stone heritage areas. We also detected various mobile genetic elements (namely mobilome, e.g., prophages, plasmids, and insertion sequences) that could accelerate replication and horizontal transfer of AMR genes. Host-tracking analysis further identified multiple biodeterioration-related bacterial genera such as Pseudonocardia, Sphingmonas, and Streptomyces as the major hosts of resistome. Taken together, these findings highlight that stone microbiota is one of the natural reservoirs of antimicrobial-resistant hazards, and the diverse resistome and mobilome carried by active biodeteriogens may improve their adaptation on stone and even deactivate the antimicrobials applied against biodeterioration. This enhanced knowledge may also provide novel and specific avenues for environmental management and stone heritage protection.
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Affiliation(s)
- Jintao He
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, China
| | - Nan Zhang
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, China
| | - Xiaoqiang Shen
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, China
| | - Abrar Muhammad
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, China
| | - Yongqi Shao
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, China; Key Laboratory for Molecular Animal Nutrition, Ministry of Education, China.
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24
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Teixeira P, Pinto N, Henriques I, Tacão M. KPC-3-, GES-5-, and VIM-1-Producing Enterobacterales Isolated from Urban Ponds. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19105848. [PMID: 35627386 PMCID: PMC9141432 DOI: 10.3390/ijerph19105848] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 01/27/2023]
Abstract
Carbapenems are antibiotics of pivotal importance in human medicine, the efficacy of which is threatened by the increasing prevalence of carbapenem-resistant Enterobacterales (CRE). Urban ponds may be reservoirs of CRE, although this hypothesis has been poorly explored. We assessed the proportion of CRE in urban ponds over a one-year period and retrieved 23 isolates. These were submitted to BOX-PCR, PFGE, 16S rDNA sequencing, antibiotic susceptibility tests, detection of carbapenemase-encoding genes, and conjugation assays. Isolates were affiliated with Klebsiella (n = 1), Raoultella (n = 11), Citrobacter (n = 8), and Enterobacter (n = 3). Carbapenemase-encoding genes were detected in 21 isolates: blaKPC (n = 20), blaGES-5 (n = 6), and blaVIM (n = 1), with 7 isolates carrying two carbapenemase genes. Clonal isolates were collected from different ponds and in different campaigns. Citrobacter F6, Raoultella N9, and Enterobacter N10 were predicted as pathogens from whole-genome sequence analysis, which also revealed the presence of several resistance genes and mobile genetic elements. We found that blaKPC-3 was located on Tn4401b (Citrobacter F6 and Enterobacter N10) or Tn4401d (Raoultella N9). The former was part of an IncFIA-FII pBK30683-like plasmid. In addition, blaGES-5 was in a class 3 integron, either chromosomal (Raoultella N9) or plasmidic (Enterobacter N10). Our findings confirmed the role of urban ponds as reservoirs and dispersal sites for CRE.
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Affiliation(s)
- Pedro Teixeira
- CESAM (Centre for Marine and Environmental Studies), University of Aveiro, 3810-193 Aveiro, Portugal; (P.T.); (M.T.)
- Biology Department, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Nuno Pinto
- Biology Department, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Isabel Henriques
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3004-531 Coimbra, Portugal
- Correspondence:
| | - Marta Tacão
- CESAM (Centre for Marine and Environmental Studies), University of Aveiro, 3810-193 Aveiro, Portugal; (P.T.); (M.T.)
- Biology Department, University of Aveiro, 3810-193 Aveiro, Portugal;
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25
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Hu X, Fu Y, Shi H, Xu W, Shen C, Hu B, Ma L, Lou L. Neglected resistance risks: Cooperative resistance of antibiotic resistant bacteria influenced by primary soil components. JOURNAL OF HAZARDOUS MATERIALS 2022; 429:128229. [PMID: 35074748 DOI: 10.1016/j.jhazmat.2022.128229] [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: 11/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Various antibiotic resistant bacteria (ARB) can thrive in soil and resist such environmental pressures as antibiotics through cooperative resistance, thereby promoting ARB retention and antibiotic resistance genes transmission. However, there has been finite knowledge in regard to the mechanisms and potential ecological risks of cooperative resistance in soil microbiome. In this study, soil minerals and organic matters were designed to treat a mixture of two Escherichia coli strains with different antibiotic resistance (E. coli DH5α/pUC19 and E. coli XL2-Blue) to determine how soil components affected cooperative resistance, and Luria-Bertani plates containing two antibiotics were used to observe dual-drug resistant bacteria (DRB) developed via cooperative resistance. Results showed quartz, humic acid, and biochar promoted E. coli XL2-Blue with high fitness costs, whereas kaolin, montmorillonite, and soot inhibited both strains. Using fluorescence microscope and PCR, it was speculated DRB could resist the antibiotic pressure via E. coli XL2-Blue coating E. coli DH5α/pUC19. E. coli DH5α/pUC19 dominated cooperative resistance. Correlation analysis and scanning electron microscope images indicated soil components influenced cooperative resistance. Biochar promoted cooperative resistance by increasing intracellular reactive oxygen species, thereby reducing the dominant strain concentration required for DRB development. Kaolin inhibited cooperative resistance the most, followed by soot and montmorillonite.
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Affiliation(s)
- Xinyi Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Yulong Fu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Hongyu Shi
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Weijian Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Chaofeng Shen
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310020, People's Republic of China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310020, People's Republic of China
| | - Liping Ma
- School of Ecological and Environmental Sciences, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, East China Normal University, Shanghai 200062, People's Republic of China.
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310020, People's Republic of China.
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26
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Matviichuk O, Mondamert L, Geffroy C, Gaschet M, Dagot C, Labanowski J. River Biofilms Microbiome and Resistome Responses to Wastewater Treatment Plant Effluents Containing Antibiotics. Front Microbiol 2022; 13:795206. [PMID: 35222329 PMCID: PMC8863943 DOI: 10.3389/fmicb.2022.795206] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/14/2022] [Indexed: 11/17/2022] Open
Abstract
Continuous exposure to low concentrations of antibiotics (sub-minimal inhibitory concentration: sub-MIC) is thought to lead to the development of antimicrobial resistance (AMR) in the environmental microbiota. However, the relationship between antibiotic exposure and resistance selection in environmental bacterial communities is still poorly understood and unproven. Therefore, we measured the concentration of twenty antibiotics, resistome quality, and analyzed the taxonomic composition of microorganisms in river biofilms collected upstream (UPS) and downstream (DWS) (at the point of discharge) from the wastewater treatment plant (WWTP) of Poitiers (France). The results of statistical analysis showed that the antibiotic content, resistome, and microbiome composition in biofilms collected UPS were statistically different from that collected DWS. According to Procrustes analysis, microbial community composition and antibiotics content may be determinants of antibiotic resistance genes (ARGs) composition in samples collected DWS. However, network analysis showed that the occurrence and concentration of antibiotics measured in biofilms did not correlate with the occurrence and abundance of antibiotic resistance genes and mobile genetic elements. In addition, network analysis suggested patterns of co-occurrence between several ARGs and three classes of bacteria/algae: Bacteroidetes incertae sedis, Cyanobacteria/Chloroplast, and Nitrospira, in biofilm collected UPS. The absence of a direct effect of antibiotics on the selection of resistance genes in the collected samples suggests that the emergence of antibiotic resistance is probably not only due to the presence of antibiotics but is a more complex process involving the cumulative effect of the interaction between the bacterial communities (biotic) and the abiotic matrix. Nevertheless, this study confirms that WWTP is an important reservoir of various ARGs, and additional efforts and legislation with clearly defined concentration limits for antibiotics and resistance determinants in WWTP effluents are needed to prevent their spread and persistence in the environment.
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Affiliation(s)
- Olha Matviichuk
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, Poitiers, France.,UMR INSERM 1092, Limoges, France
| | - Leslie Mondamert
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, Poitiers, France
| | - Claude Geffroy
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, Poitiers, France
| | | | | | - Jérôme Labanowski
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, University of Poitiers, Poitiers, France
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27
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Ning K, Ji L, Zhang L, Zhu X, Wei H, Han M, Wang Z. Is rice-crayfish co-culture a better aquaculture model: From the perspective of antibiotic resistome profiles. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118450. [PMID: 34740740 DOI: 10.1016/j.envpol.2021.118450] [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: 08/03/2021] [Revised: 10/23/2021] [Accepted: 10/30/2021] [Indexed: 05/06/2023]
Abstract
Aquaculture ecosystem is a hot-spot for antibiotic resistance genes (ARGs). Rice-crayfish co-culture was considered an eco-friendly aquaculture model and has been widely adopted in China. However, it is unclear whether rice-crayfish co-culture is one of the most eco-friendly models from the perspective of antibiotic resistance profiles. In this study, we evaluated the eco-friendliness of rice-crayfish co-culture, and compared this model with other aquaculture models, from the perspectives of antibiotics and ARG patterns, based on multi-omics and antibiotic profiles. Results showed that the nutrient levels, antibiotic concentrations, dominant microbial genera and ARG patterns in the rice-crayfish co-culture model were profoundly different from the other three aquaculture models (crab only aquaculture model, crayfish only aquaculture model, and crab-crayfish co-culture models). Specifically, the rice-crayfish co-culture model has significantly lower diversity of ARGs and lower potential risks of ARGs when compared to the other aquaculture models. Nutrient and antibiotic concentrations were the important environmental factors for shaping ARG patterns, but compared with environmental factors, the effects of mobile genes and bacteria community on the proliferation and transmission of ARGs were stronger. This study has deepened our understanding of ARGs in freshwater aquaculture ecosystem, and suggested that rice-crayfish co-culture model is a relatively eco-friendly aquaculture model when compared with the other aquaculture models.
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Affiliation(s)
- Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Lei Ji
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Lu Zhang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xue Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Huimin Wei
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Maozhen Han
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Zhi Wang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China.
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Bombaywala S, Purohit HJ, Dafale NA. Mobility of antibiotic resistance and its co-occurrence with metal resistance in pathogens under oxidative stress. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 297:113315. [PMID: 34298350 DOI: 10.1016/j.jenvman.2021.113315] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/08/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
The bacterial communities are challenged with oxidative stress during their exposure to bactericidal antibiotics, metals, and different levels of dissolved oxygen (DO) encountered in diverse environmental habitats. The frequency of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) co-selection is increased by selective pressure posed by oxidative stress. Hence, study of resistance acquisition is important from an evolutionary perspective. To understand the dependence of oxidative stress on the dissemination of ARGs and MRGs through a pathogenic bacterial population, 12 metagenomes belonging to gut, water and soil habitats were evaluated. The metagenome-wide analysis showed the chicken gut to pose the most diverse pool of ARGs (30.4 ppm) and pathogenic bacteria (Simpson diversity = 0.98). The most common types of resistances found in all the environmental samples were efflux pumps (13.22 ppm) and genes conferring resistance to vancomycin (12.4 ppm), tetracycline (12.1 ppm), or beta-lactam (9.4 ppm) antibiotics. Additionally, limiting DO level in soil was observed to increase the abundance of excision nucleases (uvrA and uvrB), DNA polymerase (polA), catalases (katG), and other oxidative stress response genes (OSGs). This was further evident from major variations occurred in antibiotic efflux genes due to the effect of DO concentration on two human pathogens, namely Salmonella enterica and Shigella sonnei found in all the selected habitats. In conclusion, the microbial community, when challenged with oxidative stress caused by environmental variations in oxygen level, tends to accumulate higher amounts of ARGs with increased dissemination potential through triggering non-lethal mutagenesis. Furthermore, the genetic linkage or co-occurrence of ARGs and MRGs provides evidence for selecting ARGs under high concentrations of heavy metals.
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Affiliation(s)
- Sakina Bombaywala
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 4400 20, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hemant J Purohit
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 4400 20, India
| | - Nishant A Dafale
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 4400 20, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Ali A, Sultan I, Mondal AH, Siddiqui MT, Gogry FA, Haq QMR. Lentic and effluent water of Delhi-NCR: a reservoir of multidrug-resistant bacteria harbouring blaCTX-M, blaTEM and blaSHV type ESBL genes. JOURNAL OF WATER AND HEALTH 2021; 19:592-603. [PMID: 34371496 DOI: 10.2166/wh.2021.085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Antimicrobial resistance is not restricted to clinics but also spreading fast in the aquatic environment. This study focused on the prevalence and diversity of extended-spectrum β-lactamase (ESBL) genes among bacteria from lentic and effluent water in Delhi-NCR, India. Phenotypic screening of 436 morphologically distinct bacterial isolates collected from diverse sites revealed that 106 (∼24%) isolates were ESBL positive. Antibiotic profiling showed that 42, 60, 78 and 59% ESBL producing isolates collected from Ghazipur slaughterhouse, Lodhi garden pond, Hauz Khas lake and Jasola wastewater treatment plant, respectively, were multidrug-resistant (MDR). The multiple antibiotic resistance (MAR) index varied from 0.20 to 0.32 among selected locations. The prevalence of ESBL gene variants blaSHV, blaTEM and blaCTX-M were found to be 17.64, 35.29 and 64%, respectively. Furthermore, the analysis of obtained gene sequences showed three variants of blaCTX-M (15, 152 and 205) and two variants of blaTEM (TEM-1 and TEM-116) among ESBL producers. The co-existence of 2-3 gene variants was recorded among 48% ESBL positive isolates. New reports from this study include the blaCTX-M gene in Acinetobacter lwoffii, Enterobacter ludwigii, Exiguobacterium mexicanum and Aeromonas caviae. Furthermore, the identification of blaTEM and blaSHV in an environmental isolate of A. caviae is a new report from India.
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Affiliation(s)
- Asghar Ali
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India E-mail: ;
| | - Insha Sultan
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India E-mail: ;
| | - Aftab Hossain Mondal
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India E-mail: ;
| | | | - Firdoos Ahmad Gogry
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India E-mail: ;
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30
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Zhang QQ, Qian H, Li PY, Zhao JQ, Sun YQ, Jin RC. Insight into the evolution of microbial community and antibiotic resistance genes in anammox process induced by copper after recovery from oxytetracycline stress. BIORESOURCE TECHNOLOGY 2021; 330:124945. [PMID: 33735733 DOI: 10.1016/j.biortech.2021.124945] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
The influence of copper ion (Cu2+) on anaerobic ammonium oxidation (anammox) performance and microbial community structures after oxytetracycline (OTC) stress recovery were assessed. Experimental results demonstrated that anammox performance were stressed by 1.0 mg L-1 Cu2+ and inhibitions were reversible with total nitrogen removal rate higher than 3.08 ± 0.2 kg N m-3 d-1. The residual OTC in the anammox sludge could combine with Cu2+ introduced and thereby retarded inhibition on performance in the presence of 2.0 mg L-1 Cu2+. Moreover, the positive relation of dominant bacterium Ca. Anammoxoglobus with the abundance of functional genes and parts of antibiotic resistance genes were observed, suggesting that regain of performance was the results of the gradual domestication of latent resistant species after inhibition. This investigation reveals new insights into resistance of anammox performance for Cu2+ and OTC.
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Affiliation(s)
- Qian-Qian Zhang
- School of Water and Environment, Chang'an University, Xi'an 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, Xi'an 710054, China
| | - Hui Qian
- School of Water and Environment, Chang'an University, Xi'an 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, Xi'an 710054, China
| | - Pei-Yue Li
- School of Water and Environment, Chang'an University, Xi'an 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, Xi'an 710054, China
| | - Jian-Qiang Zhao
- School of Water and Environment, Chang'an University, Xi'an 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, Xi'an 710054, China
| | - Ya-Qiao Sun
- School of Water and Environment, Chang'an University, Xi'an 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, Xi'an 710054, China
| | - Ren-Cun Jin
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
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31
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Ranjan VK, Mukherjee S, Basak C, Chakraborty R. Abundance of New Delhi Metallo-β-Lactamase-Producing Acinetobacter, Escherichia, Proteus, and Pseudomonas spp. in Mahananda and Karala Rivers of India. Microb Drug Resist 2021; 27:1603-1615. [PMID: 33956535 DOI: 10.1089/mdr.2019.0449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this study, we report a high incidence of New Delhi metallo-β-lactamase (NDM)-producing and ampicillin-catabolizing bacteria within carbapenem-resistant bacterial populations in the waters of two important rivers, Mahananda and Karala, bisecting two most populous towns, Siliguri and Jalpaiguri, respectively, in the northern West Bengal, India. Isolates producing NDM belonged to four genera, Acinetobacter, Escherichia, Proteus, and Pseudomonas; among which few were phylogenetically determined as putatively novel species. Class 1 integrons with the frequent presence of aadA and aac(6')-Ib gene cassettes in 50% of NDM-bearing isolates are indicative of possible selective pressures generated out of unregulated use of streptomycin, in agriculture practiced by the cultivators and tea planters living in locales drained by these two rivers, in their up- and downstream, and amikacin in the most crowded government-sponsored "sadar" and district hospitals of Siliguri and Jalpaiguri. NDM-delivering bacteria in rivers have genuine consequences for city inhabitants who are dependent on public water and sanitation facilities. Standard reconnaissance of antibiotic resistance, consolidating ecological sampling just as the assessment of clinical isolates, should be set up as a need.
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Affiliation(s)
- Vivek Kumar Ranjan
- OMICS Laboratory, Department of Biotechnology, University of North Bengal, Siliguri, India
| | - Shriparna Mukherjee
- OMICS Laboratory, Department of Biotechnology, University of North Bengal, Siliguri, India.,Department of Botany, Prasannadeb Women's College, Jalpaiguri, India
| | - Chandana Basak
- OMICS Laboratory, Department of Biotechnology, University of North Bengal, Siliguri, India
| | - Ranadhir Chakraborty
- OMICS Laboratory, Department of Biotechnology, University of North Bengal, Siliguri, India
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32
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Cherak Z, Loucif L, Moussi A, Rolain JM. Carbapenemase-producing Gram-negative bacteria in aquatic environments: a review. J Glob Antimicrob Resist 2021; 25:287-309. [PMID: 33895415 DOI: 10.1016/j.jgar.2021.03.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/04/2021] [Accepted: 03/20/2021] [Indexed: 01/05/2023] Open
Abstract
Antibiotic resistance is one of the greatest public-health challenges worldwide, especially with regard to Gram-negative bacteria (GNB). Carbapenems are the β-lactam antibiotics of choice with the broadest spectrum of activity and, in many cases, are the last-resort treatment for several bacterial infections. Carbapenemase-encoding genes, mainly carried by mobile genetic elements, are the main mechanism of resistance against carbapenems in GNB. These enzymes exhibit a versatile hydrolytic capacity and confer resistance to most β-lactam antibiotics. After being considered a clinical issue, increasing attention is being giving to the dissemination of such resistance mechanisms in the environment and especially through water. Aquatic environments are among the most significant microbial habitats on our planet, known as a favourable medium for antibiotic gene transfer, and they play a crucial role in the huge spread of drug resistance in the environment and the community. In this review, we present current knowledge regarding the spread of carbapenemase-producing isolates in different aquatic environments, which may help the implementation of control and prevention strategies against the spread of such dangerous resistant agents in the environment.
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Affiliation(s)
- Zineb Cherak
- Laboratoire de Génétique, Biotechnologie et Valorisation des Bio-ressources (GBVB), Faculté des Sciences Exactes et des Sciences de la Nature et de la Vie, Université Mohamed Khider, Biskra, Algeria
| | - Lotfi Loucif
- Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Département de Microbiologie et de Biochimie, Faculté des Sciences de la Nature et de la Vie, Université de Batna 2, Batna, Algeria.
| | - Abdelhamid Moussi
- Laboratoire de Génétique, Biotechnologie et Valorisation des Bio-ressources (GBVB), Faculté des Sciences Exactes et des Sciences de la Nature et de la Vie, Université Mohamed Khider, Biskra, Algeria
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France; IHU Méditerranée Infection, Marseille, France; and Assistance Publique des Hôpitaux de Marseille, Marseille, France
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33
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Wang P, Wu D, You X, Su Y, Xie B. Antibiotic and metal resistance genes are closely linked with nitrogen-processing functions in municipal solid waste landfills. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123689. [PMID: 32835993 DOI: 10.1016/j.jhazmat.2020.123689] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
Landfilled antibiotics and metals were related to the occurrences of their resistance genes, whose decade-long development in leachates with the dynamic landfilling environmental conditions, especially with the varying nitrogen contents, has yet to be studied. Here, we sampled leachates from five representative municipal solid waste landfills in China. The total concentrations of antibiotics (5000 - 50000 ng/L) and metals (10 - 60 mg/L) in leachates were significantly different among different sites and they were only closely related to sulfonamide and tetracycline resistance genes (P < 0.05). Regarding the abundance of subtype resistance genes, sul1 and ermB were dominant antibiotic resistance genes (ARGs) and terc, arsc, and mer were dominant heavy metal resistance genes (HMRGs); and meanwhile the observed huge variations of these genes appeared to be related to environmental factors like nitrate and pH (P < 0.05). The GeoChip results further indicated that more than 85% of sequenced ARGs/HMRGs and nitrogen processing genes, particularly of the denitrification genes, were hosted by the same bacterial species, such as Pseudomonas sp. and Bacillus sp., which belonged to the predominant phylum in leachates. These results extended our knowledge about the linkages among ARGs, HMRGs and nitrogen-processing functions in leachates.
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Affiliation(s)
- Panliang Wang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, PR China
| | - Dong Wu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, PR China
| | - Xinxin You
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, PR China
| | - Yinglong Su
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, PR China
| | - Bing Xie
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, PR China; Engineering Research Center for Nanophotonics and Advanced Instrument, Ministry of Education, East China Normal University, Shanghai, 200062, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, PR China.
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34
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Mbanga J, Abia ALK, Amoako DG, Essack SY. Longitudinal Surveillance of Antibiotic Resistance in Escherichia coli and Enterococcus spp. from a Wastewater Treatment Plant and Its Associated Waters in KwaZulu-Natal, South Africa. Microb Drug Resist 2021; 27:904-918. [PMID: 33512279 DOI: 10.1089/mdr.2020.0380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We assessed the prevalence, distribution, and antibiotic resistance patterns of Escherichia coli and Enterococcus spp. isolated from raw and treated wastewater of a major wastewater treatment plant (WWTP) in KwaZulu-Natal, South Africa and the receiving river water upstream and downstream from the WWTP discharge point. Escherichia coli and enterococci were isolated and counted using the Colilert®-18 Quanti-Tray® 2000 and Enterolert®-18 Quanti-Tray 2000 systems, respectively. A total of 580 quantitative PCR-confirmed E. coli and 579 enterococci were randomly chosen from positive samples and tested for in vitro antibiotic susceptibility using the disk diffusion assay against 20 and 16 antibiotics, respectively. The removal success of the bacterial species through the treatment procedure at the WWTP was expressed as log removal values (LRVs). Most E. coli were susceptible to meropenem (94.8%) and piperacillin-tazobactam (92.9%), with most Enterococcus susceptible to ampicillin (97.8%) and vancomycin (96.7%). In total, 376 (64.8%) E. coli and 468 (80.8%) Enterococcus isolates showed multidrug resistance (MDR). A total of 42.4% (246/580) E. coli and 65.1% (377/579) enterococci isolates had multiple antibiotic resistance indices >0.2. The LRV for E. coli ranged from 2.97 to 3.99, and for enterococci the range was observed from 1.83 to 3.98. A high proportion of MDR E. coli and enterococci were present at all sampled sites, indicating insufficient removal during wastewater treatment. There is a need to appraise the public health risks associated with bacterial contamination of environmental waters arising from such WWTPs to protect the health of users of the receiving water bodies.
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Affiliation(s)
- Joshua Mbanga
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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35
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Ojemaye MO, Adefisoye MA, Okoh AI. Nanotechnology as a viable alternative for the removal of antimicrobial resistance determinants from discharged municipal effluents and associated watersheds: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 275:111234. [PMID: 32866924 DOI: 10.1016/j.jenvman.2020.111234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 05/25/2020] [Accepted: 08/12/2020] [Indexed: 05/20/2023]
Abstract
Effective and efficient utilization of antimicrobial drugs has been one of the important cornerstone of modern medicine. However, since antibiotics were first discovered by Alexander Fleming about a century ago, the time clock of antimicrobial resistance (AMR) started ticking somewhat leading to a global fear of a possible "post-antimicrobial era". Antibiotic resistance (AR) remains a serious challenge causing global outcry in both the clinical setting and the environment. The huge influence of municipal wastewater effluent discharges on the aquatic environment has made the niche a hotspot of research interest in the study of emergence and spread of AMR microbes and their resistance determinants/genes. The current review adopted a holistic approach in studying the proliferation of antibiotic resistance determinants (ARDs) as well as their impacts and fate in municipal wastewater effluents and the receiving aquatic environments. The various strategies deployed hitherto for the removal of resistance determinants in municipal effluents were carefully reviewed, while the potential for the use of nanotechnology as a viable alternative is explicitly explored. Also, highlighted in this review are the knowledge gaps to be filled in order to curtail the spread of AMR in aquatic environment and lastly, suggestions on the applicability of nanotechnology in eliminating AMR determinants in municipal wastewater treatment facilities are proffered.
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Affiliation(s)
- Mike O Ojemaye
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, South Africa; Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, South Africa.
| | - Martins A Adefisoye
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, South Africa; Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, South Africa.
| | - Anthony I Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, South Africa; Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, South Africa.
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36
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Guo XP, Zhao S, Chen YR, Yang J, Hou LJ, Liu M, Yang Y. Antibiotic resistance genes in sediments of the Yangtze Estuary: From 2007 to 2019. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140713. [PMID: 32693274 DOI: 10.1016/j.scitotenv.2020.140713] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/01/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
To better understand the occurrence and succession of antibiotic resistance genes (ARGs) in the environment, the investigation of ARGs in sediment for a long time scale is urgently needed. In this study, sediment samples were taken in the Yangtze Estuarine area from 2007 to 2019, and the interannual variations in ARGs and their possible physicochemical and socioeconomic influencing factors were analyzed. The results showed that the abundance of ARGs, including sul1, sul2, tetM, tetW, aac(6')-Ib and qnrS, was higher in recent years (from 2015 to 2019) than that in earlier years (from 2007 to 2011), and heavier ARG pollution was found in Wusongkou (WSK) samples than in Liuhekou (LHK) samples. According to the redundancy discriminant analysis (RDA) and correlation analysis, the antibiotics (especially individual antibiotic categories, including oxytetracycline, doxycycline hyclate and norfloxacin), metals and a metal resistance gene (zntA) and total organic carbon (TOC) showed significant correlations to ARGs. In addition, antibiotics, metals, TOC and ARGs were also significantly correlated with several socioeconomic indices. Furthermore, the extended STIRPAT model analysis revealed that the second industry product and the first industry product were the major socioeconomic driver factors for the ARG distribution at WSK and LHK, respectively. Overall, with socioeconomic development, antibiotics, metals, TOC and ARGs increased in sediment. In addition, antibiotics, metals and TOC may participate in the regulation of the occurrence and distribution of ARGs in the Yangtze Estuary for the long time scale.
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Affiliation(s)
- Xing-Pan Guo
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Sai Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yu-Ru Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jing Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China; Institute of Eco-Chongming, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China; Institute of Eco-Chongming, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
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37
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Zhang S, Abbas M, Rehman MU, Huang Y, Zhou R, Gong S, Yang H, Chen S, Wang M, Cheng A. Dissemination of antibiotic resistance genes (ARGs) via integrons in Escherichia coli: A risk to human health. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115260. [PMID: 32717638 DOI: 10.1016/j.envpol.2020.115260] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
With the induction of various emerging environmental contaminants such as antibiotic resistance genes (ARGs), environment is considered as a key indicator for the spread of antimicrobial resistance (AMR). As such, the ARGs mediated environmental pollution raises a significant public health concern worldwide. Among various genetic mechanisms that are involved in the dissemination of ARGs, integrons play a vital role in the dissemination of ARGs. Integrons are mobile genetic elements that can capture and spread ARGs among environmental settings via transmissible plasmids and transposons. Most of the ARGs are found in Gram-negative bacteria and are primarily studied for their potential role in antibiotic resistance in clinical settings. As one of the most common microorganisms, Escherichia coli (E. coli) is widely studied as an indicator carrying drug-resistant genes, so this article aims to provide an in-depth study on the spread of ARGs via integrons associated with E. coli outside clinical settings and highlight their potential role as environmental contaminants. It also focuses on multiple but related aspects that do facilitate environmental pollution, i.e. ARGs from animal sources, water treatment plants situated at or near animal farms, agriculture fields, wild birds and animals. We believe that this updated study with summarized text, will facilitate the readers to understand the primary mechanisms as well as a variety of factors involved in the transmission and spread of ARGs among animals, humans, and the environment.
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Affiliation(s)
- Shaqiu Zhang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Muhammad Abbas
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, PR China; Livestock and Dairy Development Department Lahore, Punjab, 54000, Pakistan
| | - Mujeeb Ur Rehman
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Yahui Huang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Rui Zhou
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Siyue Gong
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Hong Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Shuling Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, PR China.
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Beattie RE, Bandla A, Swarup S, Hristova KR. Freshwater Sediment Microbial Communities Are Not Resilient to Disturbance From Agricultural Land Runoff. Front Microbiol 2020; 11:539921. [PMID: 33178143 PMCID: PMC7593329 DOI: 10.3389/fmicb.2020.539921] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 09/22/2020] [Indexed: 01/02/2023] Open
Abstract
Microorganisms are critically important for the function of surface water ecosystems but are frequently subjected to anthropogenic disturbances at either acute (pulse) or long-term (press) scales. Response and recovery of microbial community composition and function following pulse disturbance is well-studied in controlled, laboratory scale experiments but is less well-understood in natural environments undergoing continual press disturbance. The objectives of this study were to determine the drivers of sediment microbial compositional and functional changes in freshwaters receiving continual press disturbance from agricultural land runoff and to evaluate the ability of the native microbial community to resist disturbance related changes as a proxy for freshwater ecosystem health. Freshwater sediments were collected seasonally over 1 year in Kewaunee County, Wisconsin, a region impacted by concentrated dairy cattle farming, manure fertilization, and associated agricultural runoff which together serve as a press disturbance. Using 16S rRNA gene amplicon sequencing, we found that sediments in locations strongly impacted by intensive agriculture contain significantly higher abundances (p < 0.01) of the genera Thiobacillus, Methylotenera, Crenotrhix, Nitrospira, and Rhodoferax compared to reference sediments, and functions including nitrate reduction, nitrite reduction, and nitrogen respiration are significantly higher (p < 0.05) at locations in close proximity to large farms. Nine species-level potential human pathogens were identified in riverine sediments including Acinetobacer lwoffi and Arcobacter skirrowii, two pathogens associated with the cattle microbiome. Microbial community composition at locations in close proximity to intensive agriculture was not resistant nor resilient to agricultural runoff disturbance within 5 months post-disturbance but did reach a new, stable microbial composition. From this data, we conclude that sediment microbial community composition is sensitive and shifts in response to chemical and microbial pollution from intensive agriculture, has a low capacity to resist infiltration by non-native, harmful bacteria and, overall, the natural buffering capacity of freshwater ecosystems is unable to fully resist the impacts from agricultural press disturbance.
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Affiliation(s)
- Rachelle E. Beattie
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Aditya Bandla
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sanjay Swarup
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Department of Biological Science, National University of Singapore, Singapore, Singapore
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Qin K, Wei L, Li J, Lai B, Zhu F, Yu H, Zhao Q, Wang K. A review of ARGs in WWTPs: Sources, stressors and elimination. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2020.04.057] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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40
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Sajjad W, Rafiq M, Din G, Hasan F, Iqbal A, Zada S, Ali B, Hayat M, Irfan M, Kang S. Resurrection of inactive microbes and resistome present in the natural frozen world: Reality or myth? THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 735:139275. [PMID: 32480145 DOI: 10.1016/j.scitotenv.2020.139275] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
The present world faces a new threat of ancient microbes and resistomes that are locked in the cryosphere and now releasing upon thawing due to climate change and anthropogenic activities. The cryosphere act as the best preserving place for these microbes and resistomes that stay alive for millions of years. Current reviews extensively discussed whether the resurrection of microbes and resistomes existing in these pristine environments is true or just a hype. Release of these ancient microorganisms and naked DNA is of great concern for society as these microbes can either cause infections directly or they can interact with contemporary microorganisms and affect their fitness, survival, and mutation rate. Moreover, the contemporary microorganisms may uptake the unlocked naked DNA, which might transform non-pathogenic microorganisms into deadly antibiotic-resistant microbes. Additionally, the resurrection of glacial microorganisms can cause adverse effects on ecosystems downstream. The release of glacial pathogens and naked DNA is real and can lead to fatal outbreaks; therefore, we must prepare ourselves for the possible reemergence of diseases caused by these microbes. This study provides a scientific base for the adoption of actions by international cooperation to develop preventive measures.
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Affiliation(s)
- Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta, Pakistan
| | - Ghufranud Din
- Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Fariha Hasan
- Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Awais Iqbal
- School of Life Sciences, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou, China
| | - Sahib Zada
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Barkat Ali
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Muhammad Hayat
- Institute of Microbial Technology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao Campus, China
| | - Muhammad Irfan
- College of Dentistry, Department of Oral Biology, University of Florida, Gainesville, FL. USA
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China.
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Al Salah DMM, Ngweme GN, Laffite A, Otamonga JP, Mulaji C, Poté J. Hospital wastewaters: A reservoir and source of clinically relevant bacteria and antibiotic resistant genes dissemination in urban river under tropical conditions. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 200:110767. [PMID: 32470679 DOI: 10.1016/j.ecoenv.2020.110767] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/21/2020] [Accepted: 05/14/2020] [Indexed: 05/12/2023]
Abstract
The occurrence and dissemination of antibiotic resistant genes (ARGs) that are associated with clinical pathogens and the evaluation of associated risks are still under-investigated in developing countries under tropical conditions. In this context, cultivable and molecular approaches were performed to assess the dissemination of bacteria and the antibiotic resistance genes in aquatic environment in Kinshasa, Democratic Republic of the Congo. Cultivable approach quantified β-lactam, carbapenem resistant, and total Escherichia coli and Enterobacteriaceae in river sediments and surface waters that receive raw hospital effluents. The molecular approach utilized Quantitative Polymerase Chain Reaction (qPCR) to quantify the total bacteria and the richness of relevant bacteria (Escherichia coli, Enterococcus, and Pseudomonas), and antibiotic resistance genes (ARGs: blaOXA-48, blaCTX-M, blaIMP, blaTEM) in sediment samples. Statistical analysis were employed to highlight the significance of hospital contribution and seasonal variation of bacteria and ARGs into aquatic ecosystems in suburban municipalities of Kinshasa, Democratic Republic of the Congo. The contribution of hospitals to antibiotic resistance proliferation is higher in the dry season than during the wet season (p < 0.05). Hospital similarly contributed Escherichia coli, Enterococcus, and Pseudomonas and ARGs significantly to the sediments in both seasons (p < 0.05). The organic matter content correlated positively with E. coli (r = 0.50, p < 0.05). The total bacterial load correlated with Enterococcus, and Pseudomonas (0.49 < r < 0.69, p < 0.05). Each ARG correlated with the total bacterial load or at least one relevant bacteria (0.41 < r < 0.81, p < 0.05). Our findings confirm that hospital wastewaters contributed significantly to antibiotic resistance profile and the significance of this contribution increased in the dry season. Moreover, our analysis highlights this risk from untreated hospital wastewaters in developing countries, which presents a great threat to public health.
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Affiliation(s)
- Dhafer Mohammed M Al Salah
- University of Geneva, Faculty of Sciences, Earth and Environmental Sciences, Institute F. A. Forel and Institute of Environmental Sciences, Bd Carl-Vogt 66, CH-1211, Geneva 4, Switzerland; King Abdulaziz City for Science and Technology, Joint Centers of Excellence Program, Prince Turki the 1st St, Riyadh, 11442, Saudi Arabia
| | - Georgette N Ngweme
- School of Public Health, Faculty of Medicine, University of Kinshasa, B.P. 11850, Kinshasa XI, Congo
| | - Amandine Laffite
- University of Geneva, Faculty of Sciences, Earth and Environmental Sciences, Institute F. A. Forel and Institute of Environmental Sciences, Bd Carl-Vogt 66, CH-1211, Geneva 4, Switzerland
| | - Jean-Paul Otamonga
- Université Pédagogique Nationale (UPN), Croisement Route de Matadi et Avenue de La Libération. Quartier Binza/UPN, B.P. 8815 Kinshasa, Congo
| | - Crispin Mulaji
- Faculty of Science, Department of Chemistry, University of Kinshasa, B.P. 190, Kinshasa XI, Congo
| | - John Poté
- University of Geneva, Faculty of Sciences, Earth and Environmental Sciences, Institute F. A. Forel and Institute of Environmental Sciences, Bd Carl-Vogt 66, CH-1211, Geneva 4, Switzerland; Université Pédagogique Nationale (UPN), Croisement Route de Matadi et Avenue de La Libération. Quartier Binza/UPN, B.P. 8815 Kinshasa, Congo; Faculty of Science, Department of Chemistry, University of Kinshasa, B.P. 190, Kinshasa XI, Congo.
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Laffite A, Al Salah DMM, Slaveykova VI, Otamonga JP, Poté J. Impact of anthropogenic activities on the occurrence and distribution of toxic metals, extending-spectra β-lactamases and carbapenem resistance in sub-Saharan African urban rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138129. [PMID: 32498199 DOI: 10.1016/j.scitotenv.2020.138129] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/13/2020] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
The occurrence and dissemination of toxic metals, antibiotic resistant bacteria and their resistance genes (ARGs) in the aquatic ecosystems of sub-Saharan African countries are still understudied, despite their potential to threat human health and aquatic organisms. In this context, the co-contamination and seasonal distribution of toxic metals and ARG in river sediments receiving untreated urban sewages and hospital effluents from Kinshasa, the capital city of the Democratic Republic of the Congo were investigated. ARGs including β-lactam resistance (blaCTX-M and blaSHV), carbapenem resistance (blaVIM, blaIMP, blaKPC, blaOXA-48 and blaNDM) and total bacterial load were quantified by using quantitative polymerase chain reaction (qPCR) in total DNA extracted from sediment. The amount of toxic metals in sediments was quantified using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). The results highlight high abundance of 16S rRNA and ARGs copy numbers in sediment samples. Strong pollution of rivers by toxic metals was found, with max values (mg kg-1) of 81.85(Cr), 5.09(Co), 33.84(Ni), 203.46 (Cu), 1055.92(Zn), 324.24(Pb) and 2.96(Hg). Results also highlight the high abundance of bacterial markers (8.06 × 109-2.42 × 1012 16S rRNA/g-1 DS) as well as antibiotic resistance genes (up to 4.58 × 108 ARG. g-1 DS) in the studied rivers. Significant correlations were observed between (i) metals (except Cd and Hg) and organic matter (R > 0.60, p < 0.05); and (ii) ARGs (except blaNDM) and 16S rRNA (R > 0.57, p < 0.05) suggesting a tight link between (i) metal contamination and anthropogenic pressure and (ii) microbial contamination of river and dissemination of antibiotic resistance. Results demonstrated that multi-diffuse pollution originating from human activity contribute to the spread of toxic metals and ARGs into the aquatic ecosystems.
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Affiliation(s)
- Amandine Laffite
- Department F.-A. Forel for Environmental and Aquatic Sciences and Institute of Environmental Sciences, School of Earth and Environmental Sciences, Faculty of Science, University of Geneva, Uni Carl Vogt, 66 Boulevard Carl-Vogt, CH-1211 Geneva 4, Switzerland
| | - Dhafer Mohammed M Al Salah
- Department F.-A. Forel for Environmental and Aquatic Sciences and Institute of Environmental Sciences, School of Earth and Environmental Sciences, Faculty of Science, University of Geneva, Uni Carl Vogt, 66 Boulevard Carl-Vogt, CH-1211 Geneva 4, Switzerland; King Abdulaziz City for Science and Technology, Joint Centers of Excellence Program, Prince Turki the 1st st, Riyadh 11442, Saudi Arabia
| | - Vera I Slaveykova
- Department F.-A. Forel for Environmental and Aquatic Sciences and Institute of Environmental Sciences, School of Earth and Environmental Sciences, Faculty of Science, University of Geneva, Uni Carl Vogt, 66 Boulevard Carl-Vogt, CH-1211 Geneva 4, Switzerland
| | - Jean-Paul Otamonga
- Université Pédagogique Nationale (UPN), Croisement Route de Matadi et Avenue de la Libération, Quartier Binza/UPN, B.P. 8815 Kinshasa, Democratic Republic of the Congo
| | - John Poté
- Department F.-A. Forel for Environmental and Aquatic Sciences and Institute of Environmental Sciences, School of Earth and Environmental Sciences, Faculty of Science, University of Geneva, Uni Carl Vogt, 66 Boulevard Carl-Vogt, CH-1211 Geneva 4, Switzerland; Université Pédagogique Nationale (UPN), Croisement Route de Matadi et Avenue de la Libération, Quartier Binza/UPN, B.P. 8815 Kinshasa, Democratic Republic of the Congo; University of Kinshasa (UNIKIN), Faculty of Science, Department of Chemistry, B.P. 190 Kinshasa XI, Democratic Republic of the Congo.
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Song J, Jongmans-Hochschulz E, Mauder N, Imirzalioglu C, Wichels A, Gerdts G. The Travelling Particles: Investigating microplastics as possible transport vectors for multidrug resistant E. coli in the Weser estuary (Germany). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137603. [PMID: 32143053 DOI: 10.1016/j.scitotenv.2020.137603] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/07/2020] [Accepted: 02/25/2020] [Indexed: 06/10/2023]
Abstract
The prevalence of multidrug-resistant Gram-negative bacteria in aquatic environments has been a long withstanding health concern, namely extended-spectrum beta-lactamase (ESBL) producing Escherichia coli. Given increasing reports on microplastic (MP) pollution in these environments, it has become crucial to better understand the role of MP particles as transport vectors for such multidrug-resistant bacteria. In this study, an incubation experiment was designed where particles of both synthetic and natural material (HDPE, tyre wear, and wood) were sequentially incubated at multiple sites along a salinity gradient from the Lower Weser estuary (Germany) to the offshore island Helgoland (German Bight, North Sea). Following each incubation period, particle biofilms and water samples were assessed for ESBL-producing E. coli, first by the enrichment and detection of E. coli using Fluorocult® LMX Broth followed by cultivation on CHROMAgar™ ESBL media to select for ESBL-producers. Results showed that general E. coli populations were present on the surfaces of wood particles across all sites but none were found to produce ESBLs. Additionally, neither HDPE nor tyre wear particles were found to harbour any E. coli. Conversely, ESBL-producing E. coli were present in surrounding waters from all sites, 64% of which conferred resistances against up to 3 other antibiotic groups, additional to the beta-lactam resistances intrinsic to ESBL-producers. This study provides a first look into the potential of MP to harbour and transport multidrug-resistant E. coli across different environments and the approach serves as an important precursor to further studies on other potentially harmful MP-colonizing species.
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Affiliation(s)
- Jessica Song
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27498 Helgoland, Germany; Faculty of Engineering, Computing, and Science, Swinburne University of Technology, Sarawak Campus, 93350 Kuching, Sarawak, Malaysia.
| | - Elanor Jongmans-Hochschulz
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27498 Helgoland, Germany
| | - Norman Mauder
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Antje Wichels
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27498 Helgoland, Germany
| | - Gunnar Gerdts
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27498 Helgoland, Germany
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Chakraborty J, Sapkale V, Rajput V, Shah M, Kamble S, Dharne M. Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 194:110443. [PMID: 32155479 DOI: 10.1016/j.ecoenv.2020.110443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
Anthropogenic activities mediated antibiotic resistance genes (ARGs) in the pristine aquatic bodies (lakes) is raising concern worldwide. Long read shotgun sequencing was used to assess taxonomic diversity, distribution of ARGs and metal resistance genes (MRGs) and mobile genetic elements (MGEs) in six sites within hypersaline Lonar soda lake (India) prone to various anthropogenic activities. Proteobacteria and Euryarchaeota were dominant phyla under domain Bacteria and Archaea respectively. Higher abundance of Bacteroidetes was pragmatic at sites 18LN5 and 18LN6. Functional analysis indicated 26 broad-spectrum ARGs types, not reported earlier in this ecosystem. Abundant ARG types identified were multidrug efflux, glycopepetide, bacitracin, tetracycline and aminogylcoside resistance. Sites 18LN1 and 18LN5 depicted 167 and 160 different ARGs subtypes respectively and rpoB2, bcrA, tetA(48), mupA, ompR, patA, vanR and multidrug ABC transporter genes were present in all samples. The rpoB2 gene was dominant in 18LN1, whereas bcrA gene in 18LN2-18LN6 sites. Around 24 MRGs types were detected with higher abundance of arsenic in 18LN1 and copper in 18LN2-18LN6, signifying metal contamination linked to MRGs. The bacterial taxa Pseudomonas, Thioalkalivibrio, Burkholderia, Clostridium, Paenibacillus, Bacillus and Streptomyces were significantly associated with ARGs. This study highlights the resistomic hotspots in the lake for deploying policies for conservation efforts.
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Affiliation(s)
- Jaya Chakraborty
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India
| | - Vibhavari Sapkale
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India
| | - Manan Shah
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India
| | - Sanjay Kamble
- Chemical Engineering and Process Development (CEPD) Division, CSIR-National Chemical Laboratory (NCL), Pune, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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Ebomah KE, Okoh AI. An African perspective on the prevalence, fate and effects of carbapenem resistance genes in hospital effluents and wastewater treatment plant (WWTP) final effluents: A critical review. Heliyon 2020; 6:e03899. [PMID: 32420480 PMCID: PMC7215200 DOI: 10.1016/j.heliyon.2020.e03899] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/30/2020] [Accepted: 04/28/2020] [Indexed: 01/04/2023] Open
Abstract
This article provides an overview of the antibiotic era and discovery of earliest antibiotics until the present day state of affairs, coupled with the emergence of carbapenem-resistant bacteria. The ways of response to challenges of antibiotic resistance (AR) such as the development of novel strategies in the search of new antibiotics, designing more effective preventive measures as well as the ecology of AR have been discussed. The applications of plant extract and chemical compounds like nanomaterials which are based on recent developments in the field of antimicrobials, antimicrobial resistance (AMR), and chemotherapy were briefly discussed. The agencies responsible for environmental protection have a role to play in dealing with the climate crisis which poses an existential threat to the planet, and contributes to ecological support towards pathogenic microorganisms. The environment serves as a reservoir and also a vehicle for transmission of antimicrobial resistance genes hence, as dominant inhabitants we have to gain a competitive advantage in the battle against AMR.
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Affiliation(s)
- Kingsley Ehi Ebomah
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
| | - Anthony Ifeanyi Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
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Chen H, Li Y, Sun W, Song L, Zuo R, Teng Y. Characterization and source identification of antibiotic resistance genes in the sediments of an interconnected river-lake system. ENVIRONMENT INTERNATIONAL 2020; 137:105538. [PMID: 32028174 DOI: 10.1016/j.envint.2020.105538] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/08/2020] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
Antimicrobial resistance has been a global public health concern. The river-lake systems are one of the tightly connected terrestrial ecosystems and, appear to be reservoirs of antibiotic resistant genes (ARGs) and dispersal routes of resistant pathogens because they are easily impacted by human activities. Currently, systematic knowledge on the prevalence, transfer risk and source of ARGs in river-lake systems is largely lacking. In this study, we focused on the high-throughput profiling and source-sink relationship disentangling of ARGs in the sediments of an interconnected river-lake system (Fuhe River and its receiving Lake Baiyang in northern China). To this end, 40 surface sediments were collected for metagenomic shotgun sequencing. The profile and co-occurrence of ARGs in the sediments of the river-lake system were comprehensively characterized, as well as the mobile genetic elements (MGEs) carrying ARGs and their potential resistome dissemination risk. CrAssphage, a recently-discovered bacteriophage, was used to track human fecal pollution on the prevalence of ARGs. Meanwhile, a novel fast expectation-maximization microbial source tracking (FEAST) method was combined with linear discriminant analysis effect size method (LEfSe) for quantitatively apportioning the contribution of river sediment to the presence of ARGs in the receiving lake. Results showed abundant and diverse ARGs (24 types consisting of 510 subtypes) were detected in the sediments of the river-lake system, including some emerging ARGs such as mcr-1, tetX and carbapenemases types. Network analysis suggested non-random co-occurrence patterns of ARGs within the same type and among different types. Importantly, a number of MGE-carrying contigs were identified with jointly containing one or more ARGs, resulting in higher resistome risk potential in Lake Baiyang than many worldwide lakes. Source tracking indicated the prevalence of ARGs in the sediments of the river-lake system might be largely explained by the extent of human fecal contamination, and apportionment estimates the load transport from Fuhe River contributed more than 80% of ARGs to the receiving Lake Baiyang.
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Affiliation(s)
- Haiyang Chen
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China.
| | - Yuezhao Li
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China
| | - Wenchao Sun
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China
| | - Liuting Song
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China
| | - Rui Zuo
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China
| | - Yanguo Teng
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China.
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Petrovich ML, Zilberman A, Kaplan A, Eliraz GR, Wang Y, Langenfeld K, Duhaime M, Wigginton K, Poretsky R, Avisar D, Wells GF. Microbial and Viral Communities and Their Antibiotic Resistance Genes Throughout a Hospital Wastewater Treatment System. Front Microbiol 2020; 11:153. [PMID: 32140141 PMCID: PMC7042388 DOI: 10.3389/fmicb.2020.00153] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 01/22/2020] [Indexed: 11/16/2022] Open
Abstract
Antibiotic resistance poses a serious threat to global public health, and antibiotic resistance determinants can enter natural aquatic systems through discharge of wastewater effluents. Hospital wastewater in particular is expected to contain high abundances of antibiotic resistance genes (ARGs) compared to municipal wastewater because it contains human enteric bacteria that may include antibiotic-resistant organisms originating from hospital patients, and can also have high concentrations of antibiotics and antimicrobials relative to municipal wastewater. Viruses also play an important role in wastewater treatment systems since they can influence the bacterial community composition through killing bacteria, facilitating transduction of genetic material between organisms, and modifying the chromosomal content of bacteria as prophages. However, little is known about the fate and connections between ARGs, viruses, and their associated bacteria in hospital wastewater systems. To address this knowledge gap, we characterized the composition and persistence of ARGs, dsDNA viruses, and bacteria from influent to effluent in a pilot-scale hospital wastewater treatment system in Israel using shotgun metagenomics. Results showed that ARGs, including genes conferring resistance to antibiotics of high clinical relevance, were detected in all sampling locations throughout the pilot-scale system, with only 16% overall depletion of ARGs per genome equivalent between influent and effluent. The most common classes of ARGs detected throughout the system conferred resistance to aminoglycoside, cephalosporin, macrolide, penam, and tetracycline antibiotics. A greater proportion of total ARGs were associated with plasmid-associated genes in effluent compared to in influent. No strong associations between viral sequences and ARGs were identified in viral metagenomes from the system, suggesting that phage may not be a significant vector for ARG transfer in this system. The majority of viruses in the pilot-scale system belonged to the families Myoviridae, Podoviridae, and Siphoviridae. Gammaproteobacteria was the dominant class of bacteria harboring ARGs and the most common putative viral host in all samples, followed by Bacilli and Betaproteobacteria. In the total bacterial community, the dominant class was Betaproteobacteria for each sample. Overall, we found that a variety of different types of ARGs and viruses were persistent throughout this hospital wastewater treatment system, which can be released to the environment through effluent discharge.
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Affiliation(s)
- Morgan L. Petrovich
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
| | - Adi Zilberman
- The Water Research Center, School of The Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Aviv Kaplan
- The Water Research Center, School of The Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Gefen R. Eliraz
- The Water Research Center, School of The Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yubo Wang
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
| | - Kathryn Langenfeld
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Melissa Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Krista Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Rachel Poretsky
- Department of Biological Sciences, The University of Illinois at Chicago, Chicago, IL, United States
| | - Dror Avisar
- The Water Research Center, School of The Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - George F. Wells
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
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Abstract
Urban rivers affected by anthropogenic activities can act as reservoirs of antibiotic resistance genes (ARGs). This study aimed to describe the occurrence of selected ARGs (blaTEM, ermF, mecA, and tetA) and a class 1 integron (intI1) in an urban river in Nepal. A total of 18 water samples were collected periodically from upstream, midstream, and downstream sites along the Bagmati River over a 1-year period. All ARGs except mecA and intI1 were consistently detected by a quantitative polymerase chain reaction in the midstream and downstream sites, with concentrations ranging from 3.1 to 7.8 log copies/mL. ARG abundance was significantly lower at the upstream site (p < 0.05), reflecting the impact of anthropogenic activities on increasing concentrations of ARGs at midstream and downstream sites. Our findings demonstrate the presence of clinically relevant ARGs in the urban river water of Nepal, suggesting a need for mitigating strategies to prevent the spread of antibiotic resistance in the environment.
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Yoo K, Yoo H, Lee J, Choi EJ, Park J. Exploring the antibiotic resistome in activated sludge and anaerobic digestion sludge in an urban wastewater treatment plant via metagenomic analysis. J Microbiol 2019; 58:123-130. [DOI: 10.1007/s12275-020-9309-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/08/2019] [Accepted: 11/03/2019] [Indexed: 10/25/2022]
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Breurec S, Reynaud Y, Frank T, Farra A, Costilhes G, Weill FX, Le Hello S. Serotype distribution and antimicrobial resistance of human Salmonella enterica in Bangui, Central African Republic, from 2004 to 2013. PLoS Negl Trop Dis 2019; 13:e0007917. [PMID: 31790418 PMCID: PMC6907862 DOI: 10.1371/journal.pntd.0007917] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/12/2019] [Accepted: 11/11/2019] [Indexed: 01/30/2023] Open
Abstract
Background Limited epidemiological and antimicrobial resistance data are available on Salmonella enterica from sub-Saharan Africa. We determine the prevalence of resistance to antibiotics in isolates in the Central African Republic (CAR) between 2004 and 2013 and the genetic basis for resistance to third-generation cephalosporin (C3G). Methodology/Principal findings A total of 582 non-duplicate human clinical isolates were collected. The most common serotype was Typhimurium (n = 180, 31% of the isolates). A randomly selected subset of S. Typhimurium isolates were subtyped by clustered regularly interspaced short palindromic repeat polymorphism (CRISPOL) typing. All but one invasive isolate tested (66/68, 96%) were associated with sequence type 313. Overall, the rates of resistance were high to traditional first-line drugs (18–40%) but low to many other antimicrobials, including fluoroquinolones (one resistant isolate) and C3G (only one ESBL-producing isolate). The extended-spectrum beta-lactamase (ESBL)-producing isolate and three additional ESBL isolates from West Africa were studied by whole genome sequencing. The blaCTX-M-15 gene and the majority of antimicrobial resistance genes found in the ESBL isolate were present in a large conjugative IncHI2 plasmid highly similar (> 99% nucleotide identity) to ESBL-carrying plasmids found in Kenya (S. Typhimurium ST313) and also in West Africa (serotypes Grumpensis, Havana, Telelkebir and Typhimurium). Conclusions/Significance Although the prevalence of ESBL-producing Salmonella isolates was low in CAR, we found that a single IncHI2 plasmid-carrying blaCTX-M-15 was widespread among Salmonella serotypes from sub-Saharan Africa, which is of concern. Salmonella enterica infections are common causes of bloodstream infection in sub-Saharan Africa and associated with a high mortality rate. Levels of multidrug resistance have become alarmingly high. Then, third-generation cephalosporin (C3G) and fluoroquinolones have become standard for first-line empirical treatment. Recently, C3G-resistant Salmonella populations have emerged and spread over all continents. This resistance is mainly mediated by acquired extended-spectrum beta-lactamase (ESBL) genes carried by mobile genetic elements such as plasmids. We report here the prevalence of resistance to antibiotics in isolates in the Central African Republic (CAR) between 2004 and 2013 and the genetic basis for resistance to C3G. Overall, resistance rates to antimicrobials were low during the study period, for all classes other than conventional antimicrobials, confirming recommendations for first-line treatment based on C3G and fluoroquinolones. Only one ESBL-producing isolate was recovered. The ESBL gene and the majority of antimicrobial resistance genes found were present in a large plasmid highly similar to ESBL-carrying plasmids found in East and West Africa, highlighting its significant role in the spread of ESBL genes in Salmonella isolates in sub-Saharan Africa. These finding have implications for treatment of salmonellosis and support the growing necessity for increased microbiological surveillance based on networks of clinical laboratories in order to control dissemination of antibiotic resistance among Salmonella isolates.
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Affiliation(s)
- Sebastien Breurec
- Laboratoire de Bactériologie, Institut Pasteur, Bangui, Central African Republic
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, France
- Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles, Pointe-à-Pitre, France
- Laboratoire de Microbiologie clinique et environnementale, Centre Hospitalier Universitaire de Pointe-à-Pitre/les Abymes, Pointe-à-Pitre, France
- * E-mail:
| | - Yann Reynaud
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, France
| | - Thierry Frank
- Laboratoire de Bactériologie, Institut Pasteur, Bangui, Central African Republic
| | - Alain Farra
- Laboratoire de Bactériologie, Institut Pasteur, Bangui, Central African Republic
| | - Geoffrey Costilhes
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, World Health Organization Collaborative Centre for typing and antibiotic resistance of Salmonella, Institut Pasteur, Paris, France
| | - François-Xavier Weill
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, World Health Organization Collaborative Centre for typing and antibiotic resistance of Salmonella, Institut Pasteur, Paris, France
| | - Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, World Health Organization Collaborative Centre for typing and antibiotic resistance of Salmonella, Institut Pasteur, Paris, France
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