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Stelmaszyk L, Stange C, Hügler M, Sidhu JP, Horn H, Tiehm A. Quantification of β-lactamase producing bacteria in German surface waters with subsequent MALDI-TOF MS-based identification and β-lactamase activity assay. Heliyon 2024; 10:e27384. [PMID: 38486766 PMCID: PMC10937694 DOI: 10.1016/j.heliyon.2024.e27384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Environmental oligotrophic bacteria are suspected to be highly relevant carriers of antimicrobial resistance (AMR). However, there is a lack of validated methods for monitoring in the aquatic environment. Since extended-spectrum β-lactamases (ESBLs) play a particularly important role in the clinical sector, a culturing method based on R2A-medium spiked with different combinations of β-lactams was applied to quantify β-lactamase-producing environmental bacteria from surface waters. In German surface water samples (n = 28), oligotrophic bacteria ranging from 4.0 × 103 to 1.7 × 104 CFU per 100 mL were detected on the nutrient-poor medium spiked with 3rd generation cephalosporins and carbapenems. These numbers were 3 log10 higher compared to ESBL-producing Enterobacteriales of clinical relevance from the same water samples. A MALDI-TOF MS identification of the isolates demonstrated, that the method leads to the isolation of environmentally relevant strains with Pseudomonas, Flavobacterium, and Janthinobacterium being predominant β-lactam resistant genera. Subsequent micro-dilution antibiotic susceptibility tests (Micronaut-S test) confirmed the expression of β-lactamases. The qPCR analysis of surface waters DNA extracts showed the presence of β-lactamase genes (blaTEM, blaCMY-2, blaOXA-48, blaVIM-2, blaSHV, and blaNDM-1) at concentrations of 3.7 (±1.2) to 1.0 (±1.9) log10 gene copies per 100 mL. Overall, the results demonstrate a widespread distribution of cephalosporinase and carbapenemase enzymes in oligotrophic environmental bacteria that have to be considered as a reservoir of ARGs and contribute to the spread of antibiotic resistance.
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Affiliation(s)
- Lara Stelmaszyk
- TZW: DVGW Technologiezentrum Wasser, Department of Water Microbiology, Karlsruher Straße 84, Karlsruhe, Germany
| | - Claudia Stange
- TZW: DVGW Technologiezentrum Wasser, Department of Water Microbiology, Karlsruher Straße 84, Karlsruhe, Germany
| | - Michael Hügler
- TZW: DVGW Technologiezentrum Wasser, Department of Water Microbiology, Karlsruher Straße 84, Karlsruhe, Germany
| | - Jatinder P.S. Sidhu
- CSIRO Oceans and Atmosphere, Ecosciences Precinct, 41 Boggo Road, Brisbane, Australia
| | - Harald Horn
- Karlsruher Institut für Technologie, Engler-Bunte Institute, Wasserchemie und Wassertechnologie, Engler-Bunte-Ring 9a, Karlsruhe, Germany
| | - Andreas Tiehm
- TZW: DVGW Technologiezentrum Wasser, Department of Water Microbiology, Karlsruher Straße 84, Karlsruhe, Germany
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Jampani M, Mateo-Sagasta J, Chandrasekar A, Fatta-Kassinos D, Graham DW, Gothwal R, Moodley A, Chadag VM, Wiberg D, Langan S. Fate and transport modelling for evaluating antibiotic resistance in aquatic environments: Current knowledge and research priorities. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132527. [PMID: 37788551 DOI: 10.1016/j.jhazmat.2023.132527] [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: 11/21/2022] [Revised: 08/03/2023] [Accepted: 09/09/2023] [Indexed: 10/05/2023]
Abstract
Antibiotics have revolutionised medicine in the last century and enabled the prevention of bacterial infections that were previously deemed untreatable. However, in parallel, bacteria have increasingly developed resistance to antibiotics through various mechanisms. When resistant bacteria find their way into terrestrial and aquatic environments, animal and human exposures increase, e.g., via polluted soil, food, and water, and health risks multiply. Understanding the fate and transport of antibiotic resistant bacteria (ARB) and the transfer mechanisms of antibiotic resistance genes (ARGs) in aquatic environments is critical for evaluating and mitigating the risks of resistant-induced infections. The conceptual understanding of sources and pathways of antibiotics, ARB, and ARGs from society to the water environments is essential for setting the scene and developing an appropriate framework for modelling. Various factors and processes associated with hydrology, ecology, and climate change can significantly affect the fate and transport of ARB and ARGs in natural environments. This article reviews current knowledge, research gaps, and priorities for developing water quality models to assess the fate and transport of ARB and ARGs. The paper also provides inputs on future research needs, especially the need for new predictive models to guide risk assessment on AR transmission and spread in aquatic environments.
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Affiliation(s)
- Mahesh Jampani
- International Water Management Institute (IWMI), Battaramulla, Colombo, Sri Lanka.
| | - Javier Mateo-Sagasta
- International Water Management Institute (IWMI), Battaramulla, Colombo, Sri Lanka
| | - Aparna Chandrasekar
- UFZ - Helmholtz Centre for Environmental Research, Department Computational Hydrosystems, Leipzig, Germany; Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Despo Fatta-Kassinos
- Civil and Environmental Engineering Department and Nireas International Water Research Center, University of Cyprus, Nicosia, Cyprus
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Ritu Gothwal
- International Water Management Institute (IWMI), Battaramulla, Colombo, Sri Lanka
| | - Arshnee Moodley
- International Livestock Research Institute (ILRI), Nairobi, Kenya; Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | | | - David Wiberg
- International Water Management Institute (IWMI), Battaramulla, Colombo, Sri Lanka
| | - Simon Langan
- International Water Management Institute (IWMI), Battaramulla, Colombo, Sri Lanka
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Gorski L, Noriega AA. Comparison of Phenotype Nutritional Profiles and Phosphate Metabolism Genes in Four Serovars of Salmonella enterica from Water Sources. Microorganisms 2023; 11:2109. [PMID: 37630669 PMCID: PMC10459026 DOI: 10.3390/microorganisms11082109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The surveillance of foods for Salmonella is hindered by bias in common enrichment media where serovars implicated in human illness are outgrown by less virulent serovars. We examined four Salmonella serovars, two common in human illness (Enteritidis and Typhimurium) and two that often dominate enrichments (Give and Kentucky), for factors that might influence culture bias. The four serovars had similar growth kinetics in Tryptic Soy Broth and Buffered Peptone Water. Phenotype microarray analysis with 950 chemical substrates to assess nutrient utilization and stress resistance revealed phenotype differences between serovars. Strains of S. Enteritidis had better utilization of plant-derived sugars such as xylose, mannitol, rhamnose, and fructose, while S. Typhimurium strains were able to metabolize tagatose. Strains of S. Kentucky used more compounds as phosphorus sources and grew better with inorganic phosphate as the sole phosphorus source. The sequences of nine genes involved in phosphate metabolism were compared, and there were differences between serovars in the catalytic ATP-binding domain of the histidine kinase phoR. Analysis of the predicted PhoR amino acid sequences from additional Salmonella genomes indicated a conservation of sequences each within the Typhimurium, Give, and Enteritidis serovars. However, three different PhoR versions were observed in S. Kentucky.
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Affiliation(s)
- Lisa Gorski
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA
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Antibiotic resistance genes and bacterial community distribution patterns in pig farms. Folia Microbiol (Praha) 2022; 67:913-921. [PMID: 35781864 DOI: 10.1007/s12223-022-00988-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/24/2022] [Indexed: 11/04/2022]
Abstract
Antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, many studies have been carried out to investigate the role of gut microbiota as a pool of antibiotic resistance genes (ARGs) in human and animals. Both the structure and function of the gut bacterial community and related ARGs in pig remain unknown. In this study, we characterized the gut microbiomes and resistomes of fecal samples collected from sixteen pig farms located in sixteen cities of Shandong Province by metagenomic sequencing. Alpha diversity indicated that fecal samples from Dezhou (DZ) and Jinan (J) showed higher alpha diversity, and the lowest was from pig farms of Rizhao (RZ). Other pig farms showed similar alpha diversity. Besides, we found that the composition of gut bacterial among these pig farms varied greatly. Helcococcus massiliensis was the dominant bacterial species in pig farms of RZ and Zibo (ZB), while Prevotella sp. P5-92 occupied a superior proportion in Binzhou (BZ) and Yantai (YT). The proportion of Lactobacillus johnsonii was similar among farms of Qingdao (QD), Linyi (LY), Taian (TA), Weifang (WF), Weihai (WH), and YT. In total, 1112 ARGs were obtained and classified into 69 groups from 48 fecal samples. ARG abundance was higher in farms of Dongying (DY) and WH than others, while the lowest farms in BZ and ZB. Interestingly, it is found that BZ pig farm was exclusive, so the tetQ gene showed a higher abundance. In contrast, the load of APH(3') - IIIa in fecal samples from DY, J-1, LC, WF, and WH was high. Meanwhile, the most relevant ARGs and the corresponding microbes were screened out. Our metagenomic sequencing data provides new insights into the abundance, diversity, and structure of bacterial community in pig farms. Meanwhile, we screened ARG-carrying bacteria and explored the correlation between ARGs and bacterial community, which provide a comprehensive view of the pig fecial ARGs and microbes in different farms of Shandong.
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Chen Y, Xia Z, Li H. Metagenomic comparison of gut communities between hawksbills (Eretmochelys imbricata) and green sea turtles (Chelonia mydas). Arch Microbiol 2022; 204:450. [PMID: 35780445 DOI: 10.1007/s00203-022-03073-8] [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: 11/17/2021] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/29/2022]
Abstract
The gut microbiota is closely linked to host nutrition, immunity, and health. Here, metagenomic analysis was conducted to elucidate the taxonomic and functional diversity of gut communities from hawksbills and green sea turtles. In terms of diversity and abundance, the gut microbiota of herbivorous green sea turtles showed a higher bacterial diversity and richness than that of hawksbills. Firmicutes dominated in all groups; however, the phylum Proteobacteria showed a higher relative abundance in hawksbills. Several metabolic pathways displayed broad prevalence and high relative abundances in the two sea turtle populations. Antibiotic resistance genes (ARGs) responsible for resistance to glycopeptide and tetracycline were the most abundant in all samples. In ARGs, the subtype macB was the most abundant in the two different sea turtle populations; however, evgS, bcrA, and efrA were more abundant in the green sea turtles, while in the hawksbills, tetT and tetB(P) were more abundant. Among mobile genetic elements (MGEs), the abundance of 16 MGE types showed a significant difference between the two sea turtle populations. MGE type transposase and plasmid were the most abundant in the two sea turtle populations. Additionally, gene functions were enriched in carbohydrate esterases, glycoside hydrolases, and polysaccharide lyases in the green sea turtles, whereas genes related to glycosyltransferases and auxiliary activities were highly abundant in hawksbills. These metagenomic profiles provide further insights into the microbial diversities of the two types of sea turtles and provide valuable information for future conservation efforts.
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Affiliation(s)
- Yuan Chen
- School of Life Science, Huizhou University, No. 46 Yanda Road, Huizhou, 516007, China
| | - Zhongrong Xia
- Guangdong Huidong Sea Turtle National Nature Reserve Administration, Huidong, 516359, Guangdong, China
| | - Hongwei Li
- School of Life Science, Huizhou University, No. 46 Yanda Road, Huizhou, 516007, China.
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Haenni M, Dagot C, Chesneau O, Bibbal D, Labanowski J, Vialette M, Bouchard D, Martin-Laurent F, Calsat L, Nazaret S, Petit F, Pourcher AM, Togola A, Bachelot M, Topp E, Hocquet D. Environmental contamination in a high-income country (France) by antibiotics, antibiotic-resistant bacteria, and antibiotic resistance genes: Status and possible causes. ENVIRONMENT INTERNATIONAL 2022; 159:107047. [PMID: 34923370 DOI: 10.1016/j.envint.2021.107047] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Antimicrobial resistance (AMR) is a major global public health concern, shared by a large number of human and animal health actors. Within the framework of a One Health approach, actions should be implemented in the environmental realm, as well as the human and animal realms. The Government of France commissioned a report to provide policy and decision makers with an evidential basis for recommending or taking future actions to mitigate AMR in the environment. We first examined the mechanisms that underlie the emergence and persistence of antimicrobial resistance in the environment. This report drew up an inventory of the contamination of aquatic and terrestrial environments by AMR and antibiotics, anticipating that the findings will be representative of some other high-income countries. Effluents of wastewater treatment plants were identified as the major source of contamination on French territory, with spreading of organic waste products as a more diffuse and incidental contamination of aquatic environments. A limitation of this review is the heterogeneity of available data in space and time, as well as the lack of data for certain sources. Comparing the French Measured Environmental Concentrations (MECs) with predicted no effect concentrations (PNECs), fluoroquinolones and trimethoprim were identified as representing high and medium risk of favoring the selection of resistant bacteria in treated wastewater and in the most contaminated rivers. All other antibiotic molecules analyzed (erythromycin, clarithromycin, azithromycin, tetracycline) were at low risk of resistance selection in those environments. However, the heterogeneity of the data available impairs their full exploitation. Consequently, we listed indicators to survey AMR and antibiotics in the environment and recommended the harmonization of sampling strategies and endpoints for analyses. Finally, the objectives and methods used for the present work could comprise a useful example for how national authorities of countries sharing common socio-geographic characteristics with France could seek to better understand and define the environmental dimension of AMR in their particular settings.
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Affiliation(s)
- Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES (French Agency for Food, Environmental and Occupational Health & Safety) - Université de Lyon, Lyon, France
| | - Christophe Dagot
- Université of Limoges, RESINFIT, UMR INSERM 1092, CHU, F-87000 Limoges, France
| | - Olivier Chesneau
- Collection de l'Institut Pasteur (CIP), Microbiology Department, Institut Pasteur, Paris, France
| | - Delphine Bibbal
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Jérôme Labanowski
- Université de Poitiers, UMR CNRS 7285 IC2MP, ENSI Poitiers, Poitiers, France
| | | | - Damien Bouchard
- National Agency for Veterinary Medicinal Products, ANSES, Fougères, France
| | | | - Louisiane Calsat
- Risk Assessment Department (DER), ANSES (French Agency for Food, Environmental and Occupational Health & Safety), Maisons-Alfort, France
| | - Sylvie Nazaret
- Université de Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Fabienne Petit
- UNIROUEN, UNICAEN, CNRS, M2C, Normandie Université Rouen, France; Sorbonne Université, CNRS, EPHE, PSL, UMR METIS, Paris F-75005, France
| | | | | | - Morgane Bachelot
- ANSES (French Agency for Food, Environmental and Occupational Health & Safety), Maisons-Alfort, France
| | - Edward Topp
- Agriculture and Agri-Food Canada, and University of Western Ontario, London, ON, Canada
| | - Didier Hocquet
- UMR Chronoenvironnement CNRS 6249, Université de Bourgogne Franche-Comté, Besançon, France; Hygiène Hospitalière, Centre Hospitalier Universitaire, 25030 Besançon, France.
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Mukherjee M, Laird E, Gentry TJ, Brooks JP, Karthikeyan R. Increased Antimicrobial and Multidrug Resistance Downstream of Wastewater Treatment Plants in an Urban Watershed. Front Microbiol 2021; 12:657353. [PMID: 34108949 PMCID: PMC8181147 DOI: 10.3389/fmicb.2021.657353] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/27/2021] [Indexed: 01/21/2023] Open
Abstract
Development and spread of antimicrobial resistance (AMR) and multidrug resistance (MDR) through propagation of antibiotic resistance genes (ARG) in various environments is a global emerging public health concern. The role of wastewater treatment plants (WWTPs) as hot spots for the dissemination of AMR and MDR has been widely pointed out by the scientific community. In this study, we collected surface water samples from sites upstream and downstream of two WWTP discharge points in an urban watershed in the Bryan-College Station (BCS), Texas area, over a period of nine months. E. coli isolates were tested for resistance to ampicillin, tetracycline, sulfamethoxazole, ciprofloxacin, cephalothin, cefoperazone, gentamycin, and imipenem using the Kirby-Bauer disc diffusion method. Antimicrobial resistant heterotrophic bacteria were cultured on R2A media amended with ampicillin, ciprofloxacin, tetracycline, and sulfamethoxazole for analyzing heterotrophic bacteria capable of growth on antibiotic-containing media. In addition, quantitative real-time polymerase chain reaction (qPCR) method was used to measure eight ARG – tetA, tetW, aacA, ampC, mecA, ermA, blaTEM, and intI1 in the surface water collected at each time point. Significant associations (p < 0.05) were observed between the locations of sampling sites relative to WWTP discharge points and the rate of E. coli isolate resistance to tetracycline, ampicillin, cefoperazone, ciprofloxacin, and sulfamethoxazole together with an increased rate of isolate MDR. The abundance of antibiotic-resistant heterotrophs was significantly greater (p < 0.05) downstream of WWTPs compared to upstream locations for all tested antibiotics. Consistent with the results from the culture-based methods, the concentrations of all ARG were substantially higher in the downstream sites compared to the upstream sites, particularly in the site immediately downstream of the WWTP effluent discharges (except mecA). In addition, the Class I integron (intI1) genes were detected in high amounts at all sites and all sampling points, and were about ∼20 times higher in the downstream sites (2.5 × 107 copies/100 mL surface water) compared to the upstream sites (1.2 × 106 copies/100 mL surface water). Results suggest that the treated WWTP effluent discharges into surface waters can potentially contribute to the occurrence and prevalence of AMR in urban watersheds. In addition to detecting increased ARG in the downstream sites by qPCR, findings from this study also report an increase in viable AMR (HPC) and MDR (E. coli) in these sites. This data will benefit establishment of improved environmental regulations and practices to help manage AMR/MDR and ARG discharges into the environment, and to develop mitigation strategies and effective treatment of wastewater.
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Affiliation(s)
- Maitreyee Mukherjee
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Long Beach, MS, United States.,Department of Soil and Crop Sciences, Texas A&M University, College Station TX, United States
| | - Edward Laird
- Department of Soil and Crop Sciences, Texas A&M University, College Station TX, United States
| | - Terry J Gentry
- Department of Soil and Crop Sciences, Texas A&M University, College Station TX, United States
| | - John P Brooks
- USDA-ARS, Mississippi State, Starkville, MS, United States
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Characterization of Environmental and Cultivable Antibiotic-Resistant Microbial Communities Associated with Wastewater Treatment. Antibiotics (Basel) 2021; 10:antibiotics10040352. [PMID: 33810449 PMCID: PMC8066808 DOI: 10.3390/antibiotics10040352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 01/04/2023] Open
Abstract
Bacterial resistance to antibiotics is a growing global concern, threatening human and environmental health, particularly among urban populations. Wastewater treatment plants (WWTPs) are thought to be “hotspots” for antibiotic resistance dissemination. The conditions of WWTPs, in conjunction with the persistence of commonly used antibiotics, may favor the selection and transfer of resistance genes among bacterial populations. WWTPs provide an important ecological niche to examine the spread of antibiotic resistance. We used heterotrophic plate count methods to identify phenotypically resistant cultivable portions of these bacterial communities and characterized the composition of the culturable subset of these populations. Resistant taxa were more abundant in raw sewage and wastewater before the biological aeration treatment stage. While some antibiotic-resistant bacteria (ARB) were detectable downstream of treated wastewater release, these organisms are not enriched relative to effluent-free upstream water, indicating efficient removal during treatment. Combined culture-dependent and -independent analyses revealed a stark difference in community composition between culturable fractions and the environmental source material, irrespective of culturing conditions. Higher proportions of the environmental populations were recovered than predicted by the widely accepted 1% culturability paradigm. These results represent baseline abundance and compositional data for ARB communities for reference in future studies addressing the dissemination of antibiotic resistance associated with urban wastewater treatment ecosystems.
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Shi LD, Xu QJ, Liu JY, Han ZX, Zhu YG, Zhao HP. Will a Non-antibiotic Metalloid Enhance the Spread of Antibiotic Resistance Genes: The Selenate Story. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1004-1014. [PMID: 33356195 DOI: 10.1021/acs.est.0c05698] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The rapid emergence of antibiotic resistance genes (ARGs) has become an increasingly serious threat to public health. Previous studies illustrate the antibiotic-like effect of many substances. However, whether and how commonly used or existing non-antibiotic metalloids (e.g., selenate) would enhance ARG spread remains poorly known. Here, we tracked the long-term operation of a bioreactor continuously fed with selenate for more than 1000 days. Metagenomic sequencing identified 191 different ARGs, of which the total abundance increased significantly after the amendment of selenate. Network analyses showed that ARGs resisting multiple drugs had very similar co-occurrence patterns, implying a potentially larger health risk. Host classification not only indicated multidrug-resistant species but also distinguished the mechanism of ARG enrichment for vertical transfer and horizontal gene transfer. Genome reconstruction of an ARG host suggested that selenate and its bioreduction product selenite could stimulate the overproduction of intracellular reactive oxygen species, which was confirmed by the direct measurement. Bacterial membrane permeability, type IV pilus formation, and DNA repair and recombination were also enhanced, together facilitating the horizontal acquirement of ARGs. Overall, this study for the first time highlights the ARG emergence and dissemination induced by a non-antibiotic metalloid and identifies ARG as a factor to consider in selenate bioremediation.
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Affiliation(s)
- Ling-Dong Shi
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
- Key Lab of Water Pollution Control & Environmental Safety of Zhejiang province, Zhejiang University, Hangzhou 310058, China
| | - Qiu-Jin Xu
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Jie-Yi Liu
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Zi-Xian Han
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- State Key Lab of Regional and Urban Ecology, Research Center for Eco-environmental Research, Chinese Academy of Sciences, Beijing 100085, China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
- Key Lab of Water Pollution Control & Environmental Safety of Zhejiang province, Zhejiang University, Hangzhou 310058, China
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Wang Q, Duan YJ, Wang SP, Wang LT, Hou ZL, Cui YX, Hou J, Das R, Mao DQ, Luo Y. Occurrence and distribution of clinical and veterinary antibiotics in the faeces of a Chinese population. JOURNAL OF HAZARDOUS MATERIALS 2020; 383:121129. [PMID: 31546217 DOI: 10.1016/j.jhazmat.2019.121129] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 05/21/2023]
Abstract
Antibiotics ingested in the human gut may create selective pressure to change the composition of the gut microbiota, which could adversely effect the immune system of the host. However, the occurrence and distribution of antibiotics in the human gut remains unclear. A total population of 180 individuals, across three Chinses regions with different economic development levels, including children, adults, and elders, were sampled in 2017. A total of 19 representative antibiotics, including both clinical and veterinary antibiotics, were investigated in human faeces. While clinical use and prescriptions were the main exposure pathways for children, environmental media were the exposure pathway to adults. In addition, significant differences (P < 0.05) in antibiotic residues in human faeces were observed amongst various economic development levels, where human faeces from underdeveloped areas were mostly associated with higher levels of antibiotics. This study first to investigate the occurrence and distribution of typical antibiotics in the faeces of a Chinese population and thereby provide a reference for the intensive study of the effects and mechanisms of antibiotics on human gut microbiota.
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Affiliation(s)
- Qing Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China; Hebei Key Laboratory of Air Pollution Cause and Impact (preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Yu-Jing Duan
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Shao-Peng Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Li-Tao Wang
- Hebei Key Laboratory of Air Pollution Cause and Impact (preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Ze-Lin Hou
- Hebei Key Laboratory of Air Pollution Cause and Impact (preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Yu-Xiao Cui
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Jie Hou
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Ranjit Das
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Da-Qing Mao
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yi Luo
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China.
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Malagi I, Sampaio SC, Pinto FGS, Rosa DM, Reis RRD. Physicochemical quality of and Escherichia coli resistance profiles in urban surface waters. BRAZ J BIOL 2019; 80:661-668. [PMID: 31644659 DOI: 10.1590/1519-6984.218915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/22/2019] [Indexed: 11/22/2022] Open
Abstract
Aquatic ecosystems of urban rivers are contaminated through waste disposal, which poses a public health problem. The objective of this research was to evaluate the quality of water used for recreation and public supply of six rivers in the city of Cascavel - Paraná, including Cascavel, Quati, Bezerra, Antas, Clarito and Amambay. Samples were collected every 4 months in 2017, and their physicochemical and microbiological parameters, as well as resistance profiles of strains of Escherichia coli to antimicrobials distributed by pharmacies of the primary healthcare network, were evaluated. Parameters such as water temperature, turbidity, total nitrogen, total phosphorus, total coliforms and thermotolerant coliforms showed significant differences. The allowed limit for thermotolerant coliforms, which was set by National Environment Council, Resolution 357/2005, was exceeded in all of the six analyzed rivers. It was determined that 48.1% of E. coli strains showed resistance to nine antimicrobial tested. The highest levels of resistance were found for ampicillin (27.7%), tetracycline (27.7%) and amoxicillin (24.0%). The results of this study contribute to the understanding of the hazards associated with the contamination of springs in urban centers with wastewater containing resistant bacteria. Therefore, recovery work is necessary in these areas because of the importance of these water sources for the entire western region of Paraná state.
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Affiliation(s)
- I Malagi
- Laboratório de Pesquisa em Ciências Agroambientais, Universidade Estadual do Oeste do Paraná, Cascavel, PR, Brasil
| | - S C Sampaio
- Laboratório de Pesquisa em Ciências Agroambientais, Universidade Estadual do Oeste do Paraná, Cascavel, PR, Brasil
| | - F G S Pinto
- Programa de Pós-graduação em Conservação e Manejo de Recursos Naturais, Laboratório de Biotecnologia e Microbiologia, Universidade Estadual do Oeste do Paraná, Cascavel, PR, Brasil
| | - D M Rosa
- Laboratório de Pesquisa em Ciências Agroambientais, Universidade Estadual do Oeste do Paraná, Cascavel, PR, Brasil
| | - R R Dos Reis
- Laboratório de Pesquisa em Ciências Agroambientais, Universidade Estadual do Oeste do Paraná, Cascavel, PR, Brasil
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Lorenzo P, Adriana A, Jessica S, Carles B, Marinella F, Marta L, Luis BJ, Pierre S. Antibiotic resistance in urban and hospital wastewaters and their impact on a receiving freshwater ecosystem. CHEMOSPHERE 2018; 206:70-82. [PMID: 29730567 DOI: 10.1016/j.chemosphere.2018.04.163] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/18/2018] [Accepted: 04/27/2018] [Indexed: 06/08/2023]
Abstract
The main objective of this study was to investigate the antibiotic resistance (AR) levels in wastewater (WW) and the impact on the receiving river. Samples were collected once per season over one year in the WW of a hospital, in the raw and treated WW of two wastewater treatment plants (WWTPs), as well as upstream and downstream from the release of WWTPs effluents into the Zenne River (Belgium). Culture-dependent methods were used to quantify Escherichia coli and heterotrophic bacteria resistant to amoxicillin, sulfamethoxazole, nalidixic acid and tetracycline. Six antibiotic resistance genes (ARGs) were quantified in both particle-attached (PAB) and free-living (FLB) bacteria. Our results showed that WWTPs efficiently removed antibiotic resistant bacteria (ARB) regardless of its AR profile. The ARGs levels were the highest in the hospital WW and were significantly reduced in both WWTPs. However, ARB and ARGs abundances significantly increased into the Zenne River downstream from the WWTPs outfalls. The variation in the relative abundance of ARGs through WW treatment differed depending on the WWTP, fraction, and gene considered. The sul1 and sul2 genes in PAB fraction showed significantly higher relative abundances in the effluent compared to the influent of both WWTPs. This study demonstrated that WWTPs could be hotspots for AR spread with significant impacts on receiving freshwater ecosystems. This was the first comprehensive study investigating at the same time antibiotics occurrence, fecal bacteria indicators, heterotrophic bacterial communities, and ARGs (distinguishing PAB and FLB) to assess AR levels in WW and impacts on the receiving river.
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Affiliation(s)
- Proia Lorenzo
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Campus de la Plaine, CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium.
| | - Anzil Adriana
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Campus de la Plaine, CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Subirats Jessica
- Catalan Institute for Water Research (ICRA), c/ Emili Grahit 101, 17003 Girona, Spain
| | - Borrego Carles
- Catalan Institute for Water Research (ICRA), c/ Emili Grahit 101, 17003 Girona, Spain
| | - Farrè Marinella
- Water and Soil Quality Research Group, Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Llorca Marta
- Water and Soil Quality Research Group, Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Balcázar Jose Luis
- Catalan Institute for Water Research (ICRA), c/ Emili Grahit 101, 17003 Girona, Spain
| | - Servais Pierre
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Campus de la Plaine, CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium
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Proia L, Anzil A, Subirats J, Borrego C, Farrè M, Llorca M, Balcázar JL, Servais P. Antibiotic resistance along an urban river impacted by treated wastewaters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 628-629:453-466. [PMID: 29453174 DOI: 10.1016/j.scitotenv.2018.02.083] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Urban rivers are impacted ecosystems which may play an important role as reservoirs for antibiotic-resistant (AR) bacteria. The main objective of this study was to describe the prevalence of antibiotic resistance along a sewage-polluted urban river. Seven sites along the Zenne River (Belgium) were selected to study the prevalence of AR Escherichia coli and freshwater bacteria over a 1-year period. Culture-dependent methods were used to estimate E. coli and heterotrophic bacteria resistant to amoxicillin, sulfamethoxazole, nalidixic acid and tetracycline. The concentrations of these four antibiotics have been quantified in the studied river. The antibiotic resistance genes (ARGs), sul1, sul2, tetW, tetO, blaTEM and qnrS were also quantified in both particle-attached (PAB) and free-living (FLB) bacteria. Our results showed an effect of treated wastewaters release on the spread of antibiotic resistance along the river. Although an increase in the abundance of both AR E. coli and resistant heterotrophic bacteria was observed from upstream to downstream sites, the differences were only significant for AR E. coli. A significant positive regression was also found between AR E. coli and resistant heterotrophic bacteria. The concentration of ARGs increased from upstream to downstream sites for both particle-attached (PAB) and free-living bacteria (FLB). Particularly, a significant increase in the abundance of four among six ARGs analyzed was observed after crossing urban area. Although concentrations of tetracycline significantly correlated with tetracycline resistance genes, the antibiotic levels were likely too low to explain this correlation. The analysis of ARGs in different fractions revealed a significantly higher abundance in PAB compared to FLB for tetO and sul2 genes. This study demonstrated that urban activities may increase the spread of antibiotic resistance even in an already impacted river.
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Affiliation(s)
- Lorenzo Proia
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Campus de la Plaine, CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium.
| | - Adriana Anzil
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Campus de la Plaine, CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Jessica Subirats
- Catalan Institute for Water Research (ICRA), c/Emili Grahit 101, 17003 Girona, Spain
| | - Carles Borrego
- Catalan Institute for Water Research (ICRA), c/Emili Grahit 101, 17003 Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Marinella Farrè
- Water and Soil Quality Research Group, Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Marta Llorca
- Water and Soil Quality Research Group, Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Jose Luis Balcázar
- Catalan Institute for Water Research (ICRA), c/Emili Grahit 101, 17003 Girona, Spain
| | - Pierre Servais
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Campus de la Plaine, CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium
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Narciso-da-Rocha C, Manaia CM. Multidrug resistance phenotypes are widespread over different bacterial taxonomic groups thriving in surface water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 563-564:1-9. [PMID: 27131885 DOI: 10.1016/j.scitotenv.2016.04.062] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/08/2016] [Accepted: 04/08/2016] [Indexed: 06/05/2023]
Abstract
The environment is the original and most ancient source of the antibiotic resistance determinants that threat the human health nowadays. In the environment, water is a privileged habitat and mode of dissemination of bacteria of different origins. Freshwater bodies that cross urban areas are supposed to hold a complex mixture of both human/animal origin and strictly environmental bacteria. In this study, we were interested in unveiling the bacterial diversity in urban river transects and, simultaneously, investigate the occurrence of antibiotic resistant bacteria, in particular the multidrug resistant (MDR). With this aim, water and sediments of two rivers were sampled from an urban transect and the bacterial diversity was assessed based on 16S rRNA gene-based community analysis and, simultaneously, total heterotrophic bacteria were isolated in the presence and in the absence of antibiotics. The three predominant phyla were Proteobacteria, Bacteroidetes and Actinobacteria, in water, or Acidobacteria, in sediments. MDR bacteria were observed to belong to the predominant phyla observed in water, mostly of the classes Gamma- and Betaproteobacteria (Proteobacteria) and Sphingobacteriia and Flavobacteriia (Bacteroidetes) and belonged to genera of ubiquitous (Pseudomonas, Acinetobacter, Stenotrophomonas) or mainly environmental (Chitinophaga, Chryseobacterium) bacteria. The observation that MDR bacteria are widespread in the environment and over distinct phylogenetic lineages has two relevant implications: i) the potential of environmental bacteria as source or facilitators for antibiotic resistance acquisition; ii) the need to complement culture-independent methods with culture-based approaches in order to identify major sources of MDR profiles.
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Affiliation(s)
- Carlos Narciso-da-Rocha
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401, Porto, Portugal
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401, Porto, Portugal.
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15
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Franklin AM, Aga DS, Cytryn E, Durso LM, McLain JE, Pruden A, Roberts MC, Rothrock MJ, Snow DD, Watson JE, Dungan RS. Antibiotics in Agroecosystems: Introduction to the Special Section. JOURNAL OF ENVIRONMENTAL QUALITY 2016; 45:377-93. [PMID: 27065385 DOI: 10.2134/jeq2016.01.0023] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The presence of antibiotic drug residues, antibiotic resistant bacteria, and antibiotic resistance genes in agroecosystems has become a significant area of research in recent years and is a growing public health concern. While antibiotics are used in both human medicine and agricultural practices, the majority of their use occurs in animal production where historically they have been used for growth promotion, in addition to the prevention and treatment of disease. The widespread use of antibiotics and the application of animal wastes to agricultural lands play major roles in the introduction of antibiotic-related contamination into the environment. Overt toxicity in organisms directly exposed to antibiotics in agroecosystems is typically not a major concern because environmental concentrations are generally lower than therapeutic doses. However, the impacts of introducing antibiotic contaminants into the environment are unknown, and concerns have been raised about the health of humans, animals, and ecosystems. Despite increased research focused on the occurrence and fate of antibiotics and antibiotic resistance over the past decade, standard methods and practices for analyzing environmental samples are limited and future research needs are becoming evident. To highlight and address these issues in detail, this special collection of papers was developed with a framework of five core review papers that address the (i) overall state of science of antibiotics and antibiotic resistance in agroecosystems using a causal model, (ii) chemical analysis of antibiotics found in the environment, (iii) need for background and baseline data for studies of antibiotic resistance in agroecosystems with a decision-making tool to assist in designing research studies, as well as (iv) culture- and (v) molecular-based methods for analyzing antibiotic resistance in the environment. With a focus on the core review papers, this introduction summarizes the current state of science for analyzing antibiotics and antibiotic resistance in agroecosystems, discusses current knowledge gaps, and develops future research priorities. This introduction also contains a glossary of terms used in the core reivew papers of this special section. The purpose of the glossary is to provide a common terminology that clearly characterizes the concepts shared throughout the narratives of each review paper.
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McLain JE, Cytryn E, Durso LM, Young S. Culture-based Methods for Detection of Antibiotic Resistance in Agroecosystems: Advantages, Challenges, and Gaps in Knowledge. JOURNAL OF ENVIRONMENTAL QUALITY 2016; 45:432-40. [PMID: 27065389 DOI: 10.2134/jeq2015.06.0317] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Various culture-based methodologies are used in assessment of antibiotic resistance in samples collected in agroecosystems. Culture-based methods commonly involve isolating target bacteria on general or selective media and assessing growth in response to specific concentrations of antibiotics. The advantages of culture-based methods are multifold. In particular, isolation of bacteria is key to understanding phenotypic characteristics of isolates and their resistance patterns, and most national and international antibiotic resistance monitoring projects are isolate based. This review covers current knowledge of bacterial groups and antibiotics commonly targeted in resistance studies using bacterial culture and discusses the range in methods used, data interpretation, and factors supporting and confounding the use of culture-based methods in assessment of antibiotic resistance. Gaps in knowledge related to study design and resistance databases are discussed. Finally, a case is made for the integration of culture-based and molecular methods to better inform our understanding of antibiotic resistance in agroecosystems.
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17
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Vittecoq M, Godreuil S, Prugnolle F, Durand P, Brazier L, Renaud N, Arnal A, Aberkane S, Jean-Pierre H, Gauthier-Clerc M, Thomas F, Renaud F. Antimicrobial resistance in wildlife. J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12596] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marion Vittecoq
- Centre de recherche de la Tour du Valat; Arles France
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université de Montpellier; Montpellier France
| | - Sylvain Godreuil
- Département de Bactériologie-Virologie; Centre Hospitalier Régional Universitaire (CHRU) de Montpellier; Montpellier France
- Université de Montpellier; Montpellier France
- U 1058; INSERM; Montpellier France
| | - Franck Prugnolle
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université de Montpellier; Montpellier France
| | - Patrick Durand
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université de Montpellier; Montpellier France
| | - Lionel Brazier
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université de Montpellier; Montpellier France
| | - Nicolas Renaud
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université de Montpellier; Montpellier France
| | - Audrey Arnal
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université de Montpellier; Montpellier France
| | - Salim Aberkane
- Département de Bactériologie-Virologie; Centre Hospitalier Régional Universitaire (CHRU) de Montpellier; Montpellier France
- U 1058; INSERM; Montpellier France
| | - Hélène Jean-Pierre
- Département de Bactériologie-Virologie; Centre Hospitalier Régional Universitaire (CHRU) de Montpellier; Montpellier France
- Université de Montpellier; Montpellier France
- UMR 5119 (UM2, CNRS, IRD, IFREMER, UM); Equipe Pathogènes et Environnements; U.F.R. Pharmacie; Montpellier France
| | - Michel Gauthier-Clerc
- Centre de recherche de la Tour du Valat; Arles France
- Département Chrono-Environnement; UMR UFC/CNRS 6249 USC INRA; Université de Franche-Comté; Besançon France
| | - Frédéric Thomas
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université de Montpellier; Montpellier France
| | - François Renaud
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université de Montpellier; Montpellier France
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Ma L, Xia Y, Li B, Yang Y, Li LG, Tiedje JM, Zhang T. Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:420-7. [PMID: 26650334 DOI: 10.1021/acs.est.5b03522] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The risk associated with antibiotic resistance disseminating from animal and human feces is an urgent public issue. In the present study, we sought to establish a pipeline for annotating antibiotic resistance genes (ARGs) based on metagenomic assembly to investigate ARGs and their co-occurrence with associated genetic elements. Genetic elements found on the assembled genomic fragments include mobile genetic elements (MGEs) and metal resistance genes (MRGs). We then explored the hosts of these resistance genes and the shared resistome of pig, chicken and human fecal samples. High levels of tetracycline, multidrug, erythromycin, and aminoglycoside resistance genes were discovered in these fecal samples. In particular, significantly high level of ARGs (7762 ×/Gb) was detected in adult chicken feces, indicating higher ARG contamination level than other fecal samples. Many ARGs arrangements (e.g., macA-macB and tetA-tetR) were discovered shared by chicken, pig and human feces. In addition, MGEs such as the aadA5-dfrA17-carrying class 1 integron were identified on an assembled scaffold of chicken feces, and are carried by human pathogens. Differential coverage binning analysis revealed significant ARG enrichment in adult chicken feces. A draft genome, annotated as multidrug resistant Escherichia coli, was retrieved from chicken feces metagenomes and was determined to carry diverse ARGs (multidrug, acriflavine, and macrolide). The present study demonstrates the determination of ARG hosts and the shared resistome from metagenomic data sets and successfully establishes the relationship between ARGs, hosts, and environments. This ARG annotation pipeline based on metagenomic assembly will help to bridge the knowledge gaps regarding ARG-associated genes and ARG hosts with metagenomic data sets. Moreover, this pipeline will facilitate the evaluation of environmental risks in the genetic context of ARGs.
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Affiliation(s)
- Liping Ma
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
| | - Yu Xia
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
| | - Bing Li
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
| | - Ying Yang
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
| | - Li-Guan Li
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
| | - James M Tiedje
- Department of Plant, Soil, and Microbial Sciences, Michigan State University , East Lansing, Michigan 48824, United States
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
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Ke X, Wang C, Jing D, Zhang Y, Zhang H. Assessing water quality by ratio of the number of dominant bacterium species between surface/subsurface sediments in Haihe River Basin. MARINE POLLUTION BULLETIN 2015; 98:267-273. [PMID: 26164783 DOI: 10.1016/j.marpolbul.2015.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 05/30/2015] [Accepted: 06/01/2015] [Indexed: 06/04/2023]
Abstract
Sedimentary microorganisms can be used as a sensitive indicator of integrated aquatic environment quality assessment and indicate long-term water quality or toxicity. According to the Chinese National Standards of GB 3838-2002 and GB 18918-2002, the comprehensive water quality in Haihe River Basin has been described. Results showed that the comprehensive water quality in 6 sites, 4 sites, and 20 sites were good, bad, and medium. Furthermore, 162 dominant bacterial species were identified in surface and subsurface sediments in the 30 sampling sites. As revealed by two initial models constructed by logistic regression, the comprehensive water quality exhibited a pattern from good to bad as the ratio of the number of dominant bacterial species in surface sediments to that in subsurface sediments increased from 1 to 2.1. This finding possibly bridged a traditional gap between aquatic microbe indicators and water quality assessment or monitoring techniques.
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Affiliation(s)
- Xin Ke
- College of Energy and Environment, Shenyang Aerospace University, Shenyang 110136, China
| | - Chunyong Wang
- College of Energy and Environment, Shenyang Aerospace University, Shenyang 110136, China
| | - Debing Jing
- College of Life Sciences, Capital Normal University, Beijing 100048, China; Xiang Yang Forestry Bureau, Xiangyang 441100, China.
| | - Yun Zhang
- College of Land and Environment, Shenyang Agriculture University, Shenyang 110161, China.
| | - Haijun Zhang
- College of Energy and Environment, Shenyang Aerospace University, Shenyang 110136, China
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Microbial Toluene Removal in Hypoxic Model Constructed Wetlands Occurs Predominantly via the Ring Monooxygenation Pathway. Appl Environ Microbiol 2015; 81:6241-52. [PMID: 26150458 DOI: 10.1128/aem.01822-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 06/26/2015] [Indexed: 11/20/2022] Open
Abstract
In the present study, microbial toluene degradation in controlled constructed wetland model systems, planted fixed-bed reactors (PFRs), was queried with DNA-based methods in combination with stable isotope fractionation analysis and characterization of toluene-degrading microbial isolates. Two PFR replicates were operated with toluene as the sole external carbon and electron source for 2 years. The bulk redox conditions in these systems were hypoxic to anoxic. The autochthonous bacterial communities, as analyzed by Illumina sequencing of 16S rRNA gene amplicons, were mainly comprised of the families Xanthomonadaceae, Comamonadaceae, and Burkholderiaceae, plus Rhodospirillaceae in one of the PFR replicates. DNA microarray analyses of the catabolic potentials for aromatic compound degradation suggested the presence of the ring monooxygenation pathway in both systems, as well as the anaerobic toluene pathway in the PFR replicate with a high abundance of Rhodospirillaceae. The presence of catabolic genes encoding the ring monooxygenation pathway was verified by quantitative PCR analysis, utilizing the obtained toluene-degrading isolates as references. Stable isotope fractionation analysis showed low-level of carbon fractionation and only minimal hydrogen fractionation in both PFRs, which matches the fractionation signatures of monooxygenation and dioxygenation. In combination with the results of the DNA-based analyses, this suggests that toluene degradation occurs predominantly via ring monooxygenation in the PFRs.
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Harnisz M, Korzeniewska E, Gołaś I. The impact of a freshwater fish farm on the community of tetracycline-resistant bacteria and the structure of tetracycline resistance genes in river water. CHEMOSPHERE 2015; 128:134-41. [PMID: 25698291 DOI: 10.1016/j.chemosphere.2015.01.035] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/30/2014] [Accepted: 01/12/2015] [Indexed: 05/16/2023]
Abstract
The aim of this study was to assess the impact of a fish farm on the structure of antibiotic resistant bacteria and antibiotic resistance genes in water of Drwęca River. Samples of upstream river waters; post-production waters and treated post-production waters from fish farm; as well as downstream river waters were monitored for tetracycline resistant bacteria, tetracycline resistant genes, basic physico-chemical parameters and tetracyclines concentration. The river waters was characterized by low levels of pollution, which was determined based on water temperature, pH and concentrations of dissolved oxygen and tetracycline antibiotics. Culture-dependent (heterotrophic plate counts, counts of bacteria resistant to oxytetracycline (OTC(R)) and doxycycline (DOX(R)), minimum inhibitory concentrations for oxytetracycline and doxycycline, multidrug resistance of OTC(R) and DOX(R), qualitative composition of OTC(R) and DOX(R), prevalence of tet genes in resistant isolates) and culture-independent surveys (quantity of tet gene copies) revealed no significant differences in the abundance of antibiotic-resistant bacteria and antibiotic resistance genes between the studied samples. The only way in which the fish farm influenced water quality in the Drwęca River was by increasing the diversity of tetracycline-resistance genes. However, it should also be noted that the bacteria of the genera Aeromonas sp. and Acinetobacter sp. were able to transfer 6 out of 13 tested tet genes into Escherichiacoli, which can promote the spread of antibiotic resistance in the environment.
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Affiliation(s)
- Monika Harnisz
- Department of Environmental Microbiology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-957 Olsztyn, Poland.
| | - Ewa Korzeniewska
- Department of Environmental Microbiology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-957 Olsztyn, Poland
| | - Iwona Gołaś
- Department of Environmental Microbiology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-957 Olsztyn, Poland
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Harnisz M, Korzeniewska E, Ciesielski S, Gołaś I. tet genes as indicators of changes in the water environment: relationships between culture-dependent and culture-independent approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 505:704-11. [PMID: 25461073 DOI: 10.1016/j.scitotenv.2014.10.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/15/2014] [Accepted: 10/15/2014] [Indexed: 05/16/2023]
Abstract
The aim of this study was to identify tetracycline resistance determinants that could be used as molecular indicators of anthropogenic changes in aquatic environments. Two parallel approaches were used to examine the prevalence of tet genes: a culture-based method involving standard PCR and a method relying on quantitative PCR. The studied site was the Łyna River in Olsztyn (Poland). The culture-dependent method revealed that the concentrations of doxycycline-resistant bacteria harboring the tet(B) gene were higher in wastewater and downstream river samples than in upstream water samples. The tet(B) gene was transferred from environmental bacteria to Escherichia coli. The results generated by the culture-independent method validated statistically significant differences in tet(B) concentrations between upstream and downstream river sections, and revealed that tet(B) levels were correlated with the presence of other tetracycline resistance genes, dissolved oxygen concentrations, temperature and doxycycline concentrations in water. Our findings indicate that doxycycline-resistant bacteria, in particular E. coli harboring tet(B) or increased concentrations of tet(B), are potentially robust indicators of changes in water environments.
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Affiliation(s)
- Monika Harnisz
- Department of Environmental Microbiology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-957 Olsztyn, Poland.
| | - Ewa Korzeniewska
- Department of Environmental Microbiology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-957 Olsztyn, Poland
| | - Sławomir Ciesielski
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45G, 10-957 Olsztyn, Poland
| | - Iwona Gołaś
- Department of Environmental Microbiology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-957 Olsztyn, Poland
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Foladori P, Bruni L, Tamburini S. Toxicant inhibition in activated sludge: fractionation of the physiological status of bacteria. JOURNAL OF HAZARDOUS MATERIALS 2014; 280:758-766. [PMID: 25240645 DOI: 10.1016/j.jhazmat.2014.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/27/2014] [Accepted: 09/01/2014] [Indexed: 06/03/2023]
Abstract
In wastewater treatment plants the sensitivity of activated sludge to a toxicant depends on the toxicity test chosen, and thus the use of more than one test is suggested. The physiological status of bacteria in response to toxicants was analysed by flow cytometry to distinguish intact, permeabilised, active cells and cells disrupted. Results were compared with respirometry and bioluminescence bioassay (Vibrio fischeri). 3,5-Dichlorophenol (DCP) was used as reference xenobiotic. DCP has a strong effect on cellular integrity, causing an increase in permeabilised and disrupted cells. A reduction of 44-80% of intact cells with 6-30 mgDCP/L for 5h was found. Inhibition of active cells was 25-49%, at 6-30 mgDCP/L for 5h. The bioluminescence bioassay resulted oversensitive to DCP compared to tests based on activated sludge, while oxygen uptake rate was affected similarly to intact cells measured by flow cytometry. Landfill leachate was tested: a detrimental impact on both cellular integrity and enzymatic activity was observed. Reduction of intact cells and active cells was by 32% and 61% respectively after addition of 50% (v/v) of leachate for 5h. The flow cytometry analysis proposed here might be widely applicable in the monitoring of various toxicants and in other aquatic biosystems.
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Affiliation(s)
- P Foladori
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, via Mesiano, 77, 38123 Trento, Italy.
| | - L Bruni
- Agenzia per la Depurazione, Autonomous Province of Trento, via S. Giovanni 36, 38122 Trento, Italy
| | - S Tamburini
- Centre for Integrative Biology (CIBIO), University of Trento, Via delle Regole 101, Mattarello, 38123 Trento, Italy
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