1
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Morales-Cortés S, Sala-Comorera L, Gómez-Gómez C, Muniesa M, García-Aljaro C. CrAss-like phages are suitable indicators of antibiotic resistance genes found in abundance in fecally polluted samples. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 359:124713. [PMID: 39134166 DOI: 10.1016/j.envpol.2024.124713] [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: 05/27/2024] [Revised: 07/23/2024] [Accepted: 08/09/2024] [Indexed: 08/16/2024]
Abstract
Antibiotic resistance genes (ARGs) have been extensively observed in bacterial DNA, and more recently, in phage particles from various water sources and food items. The pivotal role played by ARG transmission in the proliferation of antibiotic resistance and emergence of new resistant strains calls for a thorough understanding of the underlying mechanisms. The aim of this study was to assess the suitability of the prototypical p-crAssphage, a proposed indicator of human fecal contamination, and the recently isolated crAssBcn phages, both belonging to the Crassvirales group, as potential indicators of ARGs. These crAss-like phages were evaluated alongside specific ARGs (blaTEM, blaCTX-M-1, blaCTX-M-9, blaVIM, blaOXA-48, qnrA, qnrS, tetW and sul1) within the total DNA and phage DNA fractions in water and food samples containing different levels of fecal pollution. In samples with high fecal load (>103 CFU/g or ml of E. coli or somatic coliphages), such as wastewater and sludge, positive correlations were found between both types of crAss-like phages and ARGs in both DNA fractions. The strongest correlation was observed between sul1 and crAssBcn phages (rho = 0.90) in sludge samples, followed by blaCTX-M-9 and p-crAssphage (rho = 0.86) in sewage samples, both in the phage DNA fraction. The use of crAssphage and crAssBcn as indicators of ARGs, considered to be emerging environmental contaminants of anthropogenic origin, is supported by their close association with the human gut. Monitoring ARGs can help to mitigate their dissemination and prevent the emergence of new resistant bacterial strains, thus safeguarding public health.
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Affiliation(s)
- Sara Morales-Cortés
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643, Prevosti Building Floor 0, E-08028, Barcelona, Spain.
| | - Laura Sala-Comorera
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643, Prevosti Building Floor 0, E-08028, Barcelona, Spain.
| | - Clara Gómez-Gómez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643, Prevosti Building Floor 0, E-08028, Barcelona, Spain.
| | - Maite Muniesa
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643, Prevosti Building Floor 0, E-08028, Barcelona, Spain.
| | - Cristina García-Aljaro
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643, Prevosti Building Floor 0, E-08028, Barcelona, Spain.
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2
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Al-Faliti M, Wang P, Smith AL, Delgado Vela J. Phage phylogeny, molecular signaling, and auxiliary antimicrobial resistance in aerobic and anaerobic membrane bioreactors. WATER RESEARCH 2024; 256:121620. [PMID: 38677036 DOI: 10.1016/j.watres.2024.121620] [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: 12/21/2023] [Revised: 03/30/2024] [Accepted: 04/14/2024] [Indexed: 04/29/2024]
Abstract
Phage emit communication signals that inform their lytic and lysogenic life cycles. However, little is known regarding the abundance and diversity of the genes associated with phage communication systems in wastewater treatment microbial communities. This study focused on phage communities within two distinct biochemical wastewater environments, specifically aerobic membrane bioreactors (AeMBRs) and anaerobic membrane bioreactors (AnMBRs) exposed to varying antibiotic concentrations. Metagenomic data from the bench-scale systems were analyzed to explore phage phylogeny, life cycles, and genetic capacity for antimicrobial resistance and quorum sensing. Two dominant phage families, Schitoviridae and Peduoviridae, exhibited redox-dependent dynamics. Schitoviridae prevailed in anaerobic conditions, while Peduoviridae dominated in aerobic conditions. Notably, the abundance of lytic and lysogenic proteins varied across conditions, suggesting the coexistence of both life cycles. Furthermore, the presence of antibiotic resistance genes (ARGs) within viral contigs highlighted the potential for phage to transfer ARGs in AeMBRs. Finally, quorum sensing genes in the virome of AeMBRs indicated possible molecular signaling between phage and bacteria. Overall, this study provides insights into the dynamics of viral communities across varied redox conditions in MBRs. These findings shed light on phage life cycles, and auxiliary genetic capacity such as antibiotic resistance and bacterial quorum sensing within wastewater treatment microbial communities.
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Affiliation(s)
- Mitham Al-Faliti
- Department of Civil and Environmental Engineering, Howard University, Washington, D.C., USA
| | - Phillip Wang
- Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | - Adam L Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | - Jeseth Delgado Vela
- Department of Civil and Environmental Engineering, Howard University, Washington, D.C., USA.
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3
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Liu F, Luo Y, Xu T, Lin H, Qiu Y, Li B. Current examining methods and mathematical models of horizontal transfer of antibiotic resistance genes in the environment. Front Microbiol 2024; 15:1371388. [PMID: 38638913 PMCID: PMC11025395 DOI: 10.3389/fmicb.2024.1371388] [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: 01/16/2024] [Accepted: 03/11/2024] [Indexed: 04/20/2024] Open
Abstract
The increasing prevalence of antibiotic resistance genes (ARGs) in the environment has garnered significant attention due to their health risk to human beings. Horizontal gene transfer (HGT) is considered as an important way for ARG dissemination. There are four general routes of HGT, including conjugation, transformation, transduction and vesiduction. Selection of appropriate examining methods is crucial for comprehensively understanding characteristics and mechanisms of different HGT ways. Moreover, combined with the results obtained from different experimental methods, mathematical models could be established and serve as a powerful tool for predicting ARG transfer dynamics and frequencies. However, current reviews of HGT for ARG spread mainly focus on its influencing factors and mechanisms, overlooking the important roles of examining methods and models. This review, therefore, delineated four pathways of HGT, summarized the strengths and limitations of current examining methods, and provided a comprehensive summing-up of mathematical models pertaining to three main HGT ways of conjugation, transformation and transduction. Finally, deficiencies in current studies were discussed, and proposed the future perspectives to better understand and assess the risks of ARG dissemination through HGT.
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Affiliation(s)
- Fan Liu
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China
| | - Yuqiu Luo
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China
| | - Tiansi Xu
- School of Environment, Tsinghua University, Beijing, China
| | - Hai Lin
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China
| | - Yong Qiu
- School of Environment, Tsinghua University, Beijing, China
| | - Bing Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China
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4
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Stanton IC, Tipper HJ, Chau K, Klümper U, Subirats J, Murray AK. Does Environmental Exposure to Pharmaceutical and Personal Care Product Residues Result in the Selection of Antimicrobial-Resistant Microorganisms, and is this Important in Terms of Human Health Outcomes? ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024; 43:623-636. [PMID: 36416260 DOI: 10.1002/etc.5498] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/14/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The environment plays a critical role in the development, dissemination, and transmission of antimicrobial resistance (AMR). Pharmaceuticals and personal care products (PPCPs) enter the environment through direct application to the environment and through anthropogenic pollution. Although there is a growing body of evidence defining minimal selective concentrations (MSCs) of antibiotics and the role antibiotics play in horizontal gene transfer (HGT), there is limited evidence on the role of non-antibiotic PPCPs. Existing data show associations with the development of resistance or effects on bacterial growth rather than calculating selective endpoints. Research has focused on laboratory-based systems rather than in situ experiments, although PPCP concentrations found throughout wastewater, natural water, and soil environments are often within the range of laboratory-derived MSCs and at concentrations shown to promote HGT. Increased selection and HGT of AMR by PPCPs will result in an increase in total AMR abundance in the environment, increasing the risk of exposure and potential transmission of environmental AMR to humans. There is some evidence to suggest that humans can acquire resistance from environmental settings, with water environments being the most frequently studied. However, because this is currently limited, we recommend that more evidence be gathered to understand the risk the environment plays in regard to human health. In addition, we recommend that future research efforts focus on MSC-based experiments for non-antibiotic PPCPS, particularly in situ, and investigate the effect of PPCP mixtures on AMR. Environ Toxicol Chem 2024;43:623-636. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
| | | | - Kevin Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Uli Klümper
- Institute of Hydrobiology, Technische Universitӓt Dresden, Dresden, Germany
| | - Jessica Subirats
- Institute of Environmental Assessment and Water Research, Spanish Council for Scientific Research (IDAEA-CSIC), Barcelona, Spain
| | - Aimee K Murray
- College of Medicine and Health, University of Exeter, Cornwall, UK
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5
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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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6
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Gunjyal N, Singh G, Ojha CSP. Elevated levels of anthropogenic antibiotic resistance gene marker, sul1, linked with extreme fecal contamination and poor water quality in wastewater-receiving ponds. JOURNAL OF ENVIRONMENTAL QUALITY 2023; 52:652-664. [PMID: 36716263 DOI: 10.1002/jeq2.20453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/12/2023] [Indexed: 05/06/2023]
Abstract
In several low- and middle-income countries, such as India, the rapid construction of toilets to combat open defecation has not been matched with adequate wastewater treatment, resulting in extreme fecal contamination of the receiving environments. The sewage-receiving surface water bodies, typically close to the residences, are a potential hotspot for disease transmission and antibiotic resistance. Water, soil, and sediment samples from seven wastewater-receiving ponds (WRPs) were analyzed for water quality, chlorophyll-a, fecal contamination (yccT for Escherichia coli), 16S rRNA gene copies, and anthropogenic antibiotic resistance gene markers-sul1 and intI1. These WRPs were contrasted with two ponds that did not directly receive sewage. The water quality in the WRPs was comparable to raw sewage (BOD: 210-380 mg/L; COD: 350-630 mg/L; total-N: 100-190 mg/L; and total-P: 6-21 mg/L), and the relative levels of the DNA marker of E. coli were very high (yccT: 0.1% to ∼100% of total bacterial count) indicating extreme fecal contamination. The relative levels of sul1 and intI1 were 1-3 orders of magnitude higher in WRPs (sul1: 0.32%-10% of total bacterial count; and intI1: 0.2%-5% of total bacterial count) compared to the ponds that did not receive sewage directly. The relative levels of sul1 correlated with the DNA marker for the fecal indicator, E. coli (p-value < 0.05; r = 0.50; Spearman's rank correlation), and poor water quality.
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Affiliation(s)
- Neelam Gunjyal
- Department of Civil Engineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Gargi Singh
- Department of Civil Engineering, Indian Institute of Technology Roorkee, Roorkee, India
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7
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Blanco-Picazo P, Morales-Cortes S, Ramos-Barbero MD, García-Aljaro C, Rodríguez-Rubio L, Muniesa M. Dominance of phage particles carrying antibiotic resistance genes in the viromes of retail food sources. THE ISME JOURNAL 2023; 17:195-203. [PMID: 36289309 PMCID: PMC9860054 DOI: 10.1038/s41396-022-01338-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
Abstract
The growth of antibiotic resistance has stimulated interest in understanding the mechanisms by which antibiotic resistance genes (ARG) are mobilized. Among them, studies analyzing the presence of ARGs in the viral fraction of environmental, food and human samples, and reporting bacteriophages as vehicles of ARG transmission, have been the focus of increasing research. However, it has been argued that in these studies the abundance of phages carrying ARGs has been overestimated due to experimental contamination with non-packaged bacterial DNA or other elements such as outer membrane vesicles (OMVs). This study aims to shed light on the extent to which phages, OMVs or contaminating non-packaged DNA contribute as carriers of ARGs in the viromes. The viral fractions of three types of food (chicken, fish, and mussels) were selected as sources of ARG-carrying phage particles, whose ability to infect and propagate in an Escherichia coli host was confirmed after isolation. The ARG-containing fraction was further purified by CsCl density gradient centrifugation and, after removal of DNA outside the capsids, ARGs inside the particles were confirmed. The purified fraction was stained with SYBR Gold, which allowed the visualization of phage capsids attached to and infecting E. coli cells. Phages with Myoviridae and Siphoviridae morphology were observed by electron microscopy. The proteins in the purified fraction belonged predominantly to phages (71.8% in fish, 52.9% in mussels, 78.7% in chicken sample 1, and 64.1% in chicken sample 2), mainly corresponding to tail, capsid, and other structural proteins, whereas membrane proteins, expected to be abundant if OMVs were present, accounted for only 3.8-21.4% of the protein content. The predominance of phage particles in the viromes supports the reliability of the protocols used in this study and in recent findings on the abundance of ARG-carrying phage particles.
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Affiliation(s)
- Pedro Blanco-Picazo
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Edificio Prevosti. Planta 0, E-08028 Barcelona, Spain
| | - Sara Morales-Cortes
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Edificio Prevosti. Planta 0, E-08028 Barcelona, Spain
| | - María Dolores Ramos-Barbero
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Edificio Prevosti. Planta 0, E-08028 Barcelona, Spain ,grid.5268.90000 0001 2168 1800Departmento de Fisiologia, Genética y Microbiología, Universidad de Alicante (UA), 03080 Alicante, Spain
| | - Cristina García-Aljaro
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Edificio Prevosti. Planta 0, E-08028 Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Edificio Prevosti. Planta 0, E-08028 Barcelona, Spain
| | - Maite Muniesa
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Edificio Prevosti. Planta 0, E-08028 Barcelona, Spain
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8
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Clark JR, Terwilliger A, Avadhanula V, Tisza M, Cormier J, Javornik-Cregeen S, Ross MC, Hoffman KL, Troisi C, Hanson B, Petrosino J, Balliew J, Piedra PA, Rios J, Deegan J, Bauer C, Wu F, Mena KD, Boerwinkle E, Maresso AW. Wastewater pandemic preparedness: Toward an end-to-end pathogen monitoring program. Front Public Health 2023; 11:1137881. [PMID: 37026145 PMCID: PMC10070845 DOI: 10.3389/fpubh.2023.1137881] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/09/2023] [Indexed: 04/08/2023] Open
Abstract
Molecular analysis of public wastewater has great potential as a harbinger for community health and health threats. Long-used to monitor the presence of enteric viruses, in particular polio, recent successes of wastewater as a reliable lead indicator for trends in SARS-CoV-2 levels and hospital admissions has generated optimism and emerging evidence that similar science can be applied to other pathogens of pandemic potential (PPPs), especially respiratory viruses and their variants of concern (VOC). However, there are substantial challenges associated with implementation of this ideal, namely that multiple and distinct fields of inquiry must be bridged and coordinated. These include engineering, molecular sciences, temporal-geospatial analytics, epidemiology and medical, and governmental and public health messaging, all of which present their own caveats. Here, we outline a framework for an integrated, state-wide, end-to-end human pathogen monitoring program using wastewater to track viral PPPs.
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Affiliation(s)
- Justin R. Clark
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Austen Terwilliger
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Michael Tisza
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Juwan Cormier
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Sara Javornik-Cregeen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Matthew Clayton Ross
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Kristi Louise Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Catherine Troisi
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Blake Hanson
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Center for Infectious Diseases, Department of Epidemiology, Human Genetics and Environmental Sciences, Houston, TX, United States
| | - Joseph Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - John Balliew
- El Paso Water Utility, El Paso, TX, United States
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Pediatrics Department, Baylor College of Medicine, Houston, TX, United States
| | - Janelle Rios
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Jennifer Deegan
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Cici Bauer
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Department of Biostatistics and Data Science, UTHealth School of Public Health, Houston, TX, United States
| | - Fuqing Wu
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Kristina D. Mena
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Eric Boerwinkle
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, Houston, TX, United States
| | - Anthony W. Maresso
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Anthony W. Maresso
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9
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Prieto Riquelme M, Garner E, Gupta S, Metch J, Zhu N, Blair MF, Arango-Argoty G, Maile-Moskowitz A, Li AD, Flach CF, Aga DS, Nambi IM, Larsson DGJ, Bürgmann H, Zhang T, Pruden A, Vikesland PJ. Demonstrating a Comprehensive Wastewater-Based Surveillance Approach That Differentiates Globally Sourced Resistomes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14982-14993. [PMID: 35759608 PMCID: PMC9631994 DOI: 10.1021/acs.est.1c08673] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Wastewater-based surveillance (WBS) for disease monitoring is highly promising but requires consistent methodologies that incorporate predetermined objectives, targets, and metrics. Herein, we describe a comprehensive metagenomics-based approach for global surveillance of antibiotic resistance in sewage that enables assessment of 1) which antibiotic resistance genes (ARGs) are shared across regions/communities; 2) which ARGs are discriminatory; and 3) factors associated with overall trends in ARGs, such as antibiotic concentrations. Across an internationally sourced transect of sewage samples collected using a centralized, standardized protocol, ARG relative abundances (16S rRNA gene-normalized) were highest in Hong Kong and India and lowest in Sweden and Switzerland, reflecting national policy, measured antibiotic concentrations, and metal resistance genes. Asian versus European/US resistomes were distinct, with macrolide-lincosamide-streptogramin, phenicol, quinolone, and tetracycline versus multidrug resistance ARGs being discriminatory, respectively. Regional trends in measured antibiotic concentrations differed from trends expected from public sales data. This could reflect unaccounted uses, captured only by the WBS approach. If properly benchmarked, antibiotic WBS might complement public sales and consumption statistics in the future. The WBS approach defined herein demonstrates multisite comparability and sensitivity to local/regional factors.
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Affiliation(s)
| | - Emily Garner
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
- Department
of Civil and Environmental Engineering, West Virginia University, Morgantown, West Virginia26506, United States
| | - Suraj Gupta
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
- The
Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational
Biology, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Jake Metch
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Ni Zhu
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Matthew F. Blair
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Gustavo Arango-Argoty
- Department
of Computer Science, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Ayella Maile-Moskowitz
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - An-dong Li
- Department
of Civil Engineering, The University of
Hong Kong, Pokfulam, Hong Kong
| | - Carl-Fredrik Flach
- Centre for
Antibiotic Resistance Research (CARe), University
of Gothenburg, 405 30Göteborg, Sweden
- Department
of Infectious Diseases, University of Gothenburg, 405 30Göteborg, Sweden
| | - Diana S. Aga
- Department
of Chemistry, University at Buffalo, Buffalo, New York14260, United States
| | - Indumathi M. Nambi
- Department
of Civil Engineering, Indian Institute of
Technology, Madras,
Chennai600036, India
| | - D. G. Joakim Larsson
- Centre for
Antibiotic Resistance Research (CARe), University
of Gothenburg, 405 30Göteborg, Sweden
- Department
of Infectious Diseases, University of Gothenburg, 405 30Göteborg, Sweden
| | - Helmut Bürgmann
- Eawag:
Swiss Federal Institute of Aquatic Science and Technology, CH-6047Kastanienbaum, Switzerland
| | - Tong Zhang
- Department
of Civil Engineering, The University of
Hong Kong, Pokfulam, Hong Kong
| | - Amy Pruden
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Peter J. Vikesland
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
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10
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Blanco-Picazo P, Gómez-Gómez C, Tormo M, Ramos-Barbero MD, Rodríguez-Rubio L, Muniesa M. Prevalence of bacterial genes in the phage fraction of food viromes. Food Res Int 2022; 156:111342. [DOI: 10.1016/j.foodres.2022.111342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/15/2022] [Accepted: 05/03/2022] [Indexed: 11/04/2022]
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11
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Blanco-Picazo P, Gómez-Gómez C, Aguiló-Castillo S, Fernández-Orth D, Cerdà-Cuéllar M, Muniesa M, Rodríguez-Rubio L. Chicken liver is a potential reservoir of bacteriophages and phage-derived particles containing antibiotic resistance genes. Microb Biotechnol 2022; 15:2464-2475. [PMID: 35485188 PMCID: PMC9437878 DOI: 10.1111/1751-7915.14056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/15/2022] [Indexed: 11/30/2022] Open
Abstract
Poultry meat production is one of the most important agri‐food industries in the world. The selective pressure exerted by widespread prophylactic or therapeutic use of antibiotics in intensive chicken farming favours the development of drug resistance in bacterial populations. Chicken liver, closely connected with the intestinal tract, has been directly involved in food‐borne infections and found to be contaminated with pathogenic bacteria, including Campylobacter and Salmonella. In this study, 74 chicken livers, divided into sterile and non‐sterile groups, were analysed, not only for microbial indicators but also for the presence of phages and phage particles containing antibiotic resistance genes (ARGs). Both bacteria and phages were detected in liver tissues, including those dissected under sterile conditions. The phages were able to infect Escherichia coli and showed a Siphovirus morphology. The chicken livers contained from 103 to 106 phage particles per g, which carried a range of ARGs (blaTEM, blaCTx‐M‐1, sul1, qnrA, armA and tetW) detected by qPCR. The presence of phages in chicken liver, mostly infecting E. coli, was confirmed by metagenomic analysis, although this technique was not sufficiently sensitive to identify ARGs. In addition, ARG‐carrying phages were detected in chicken faeces by qPCR in a previous study of the group. Comparison of the viromes of faeces and liver showed a strong coincidence of species, which suggests that the phages found in the liver originate in faeces. These findings suggests that phages, like bacteria, can translocate from the gut to the liver, which may therefore constitute a potential reservoir of antibiotic resistance genes.
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Affiliation(s)
- Pedro Blanco-Picazo
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643, Planta 0, Barcelona, 08028, Spain
| | - Clara Gómez-Gómez
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643, Planta 0, Barcelona, 08028, Spain
| | - Sergi Aguiló-Castillo
- Spanish National Bioinformatics Institute (INB)/ELIXIR-ES, Barcelona Supercomputing Center, Barcelona, Spain
| | - Dietmar Fernández-Orth
- Department of Bioinformatics and Molecular Biology, Cerba Internacional Pl. Ramon Llull, 7-10, Sabadell, Barcelona, 08203, Spain
| | - Marta Cerdà-Cuéllar
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Maite Muniesa
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643, Planta 0, Barcelona, 08028, Spain
| | - Lorena Rodríguez-Rubio
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643, Planta 0, Barcelona, 08028, Spain
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12
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Nogueira WG, Gois BVA, Pinheiro KDC, Aragão ADO, Queiroz ALC, da Silva AL, Folador AC, Ramos RTJ. Viral Metagenomics Reveals Widely Diverse Viral Community of Freshwater Amazonian Lake. Front Public Health 2022; 10:869886. [PMID: 35548089 PMCID: PMC9081339 DOI: 10.3389/fpubh.2022.869886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/24/2022] [Indexed: 11/28/2022] Open
Abstract
Despite the importance of understanding the ecology of freshwater viruses, there are not many studies on the subject compared to marine viruses. The microbiological interactions in these environments are still poorly known, especially between bacteriophages and their host bacteria and between cyanophages and cyanobacteria. Lake Bologna, Belém, capital of the Brazilian State of Pará, is a water source that supplies the city and its metropolitan region. However, it remains unexplored regarding the contents of its virome and viral diversity composition. Therefore, this work aims to explore the taxonomic diversity of DNA viruses in this lake, especially bacteriophages and cyanophages, since they can act as transducers of resistance genes and reporters of water quality for human consumption. We used metagenomic sequencing data generated by previous studies. We analyzed it at the taxonomic level using the tools Kraken2, Bracken, and Pavian; later, the data was assembled using Genome Detective, which performs the assembly of viruses. The results observed here suggest the existence of a widely diverse viral community and established microbial phage-regulated dynamics in Lake Bolonha. This work is the first ever to describe the virome of Lake Bolonha using a metagenomic approach based on high-throughput sequencing, as it contributes to the understanding of water-related public health concerns regarding the spreading of antibiotic resistance genes and population control of native bacteria and cyanobacteria.
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Affiliation(s)
| | | | | | - Andressa de Oliveira Aragão
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Brazil
| | | | - Artur Luiz da Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Brazil
| | - Adriana Carneiro Folador
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Brazil
| | - Rommel Thiago Jucá Ramos
- Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- *Correspondence: Rommel Thiago Jucá Ramos
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13
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Blanco-Picazo P, Gómez-Gómez C, Morales-Cortes S, Muniesa M, Rodríguez-Rubio L. Antibiotic resistance in the viral fraction of dairy products and a nut-based milk. Int J Food Microbiol 2022; 367:109590. [PMID: 35220008 DOI: 10.1016/j.ijfoodmicro.2022.109590] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 10/19/2022]
Abstract
Phages, the most abundant biological entities in the biosphere, can carry different bacterial genes, including those conferring antibiotic resistance. In this study, dairy products were analyzed by qPCR for the presence of phages and phage particles containing antibiotic resistance genes (ARGs). Eleven ARGs were identified in 50 samples of kefir, yogurt, milk, fresh cheese and nut-based milk (horchata), purchased from local retailers in Barcelona. Propagation experiments showed that at least some of the phages isolated from these samples infected Escherichia coli WG5, which was selected as the host strain because it does not contain prophages or ARGs in its genome. Electron microscopy revealed that the phage particles showed morphologies compatible with the Myoviridae and Siphoviridae families. Our results show that dairy products contain ARGs within infectious phage particles and may therefore serve as a reservoir of ARGs that can be mobilized to susceptible hosts, both in the food matrix and in the intestinal tract after ingestion.
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Affiliation(s)
- Pedro Blanco-Picazo
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain
| | - Clara Gómez-Gómez
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain
| | - Sara Morales-Cortes
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain.
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14
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Chau KK, Barker L, Budgell EP, Vihta KD, Sims N, Kasprzyk-Hordern B, Harriss E, Crook DW, Read DS, Walker AS, Stoesser N. Systematic review of wastewater surveillance of antimicrobial resistance in human populations. ENVIRONMENT INTERNATIONAL 2022; 162:107171. [PMID: 35290866 PMCID: PMC8960996 DOI: 10.1016/j.envint.2022.107171] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 01/23/2022] [Accepted: 02/28/2022] [Indexed: 05/05/2023]
Abstract
OBJECTIVES We systematically reviewed studies using wastewater for AMR surveillance in human populations, to determine: (i) evidence of concordance between wastewater-human AMR prevalence estimates, and (ii) methodological approaches which optimised identifying such an association, and which could be recommended as standard. We used Lin's concordance correlation coefficient (CCC) to quantify concordance between AMR prevalence estimates in wastewater and human compartments (where CCC = 1 reflects perfect concordance), and logistic regression to identify study features (e.g. sampling methods) associated with high agreement studies (defined as >70% of within-study wastewater-human AMR prevalence comparisons within ±10%). RESULTS Of 8,867 records and 441 full-text methods reviewed, 33 studies were included. AMR prevalence data was extractable from 24 studies conducting phenotypic-only (n = 7), genotypic-only (n = 1) or combined (n = 16) AMR detection. Overall concordance of wastewater-human AMR prevalence estimates was reasonably high for both phenotypic (CCC = 0.85 [95% CI 0.8-0.89]) and genotypic approaches (CCC = 0.88 (95% CI 0.84-0.9)) despite diverse study designs, bacterial species investigated and phenotypic/genotypic targets. No significant relationships between methodological approaches and high agreement studies were identified using logistic regression; however, this was limited by inconsistent reporting of study features, significant heterogeneity in approaches and limited sample size. Based on a secondary, descriptive synthesis, studies conducting composite sampling of wastewater influent, longitudinal sampling >12 months, and time-/location-matched sampling of wastewater and human compartments generally had higher agreement. CONCLUSION Wastewater-based surveillance of AMR appears promising, with high overall concordance between wastewater and human AMR prevalence estimates in studies irrespective of heterogenous approaches. However, our review suggests future work would benefit from: time-/location-matched sampling of wastewater and human populations, composite sampling of influent, and sampling >12 months for longitudinal studies. Further research and clear and consistent reporting of study methods is required to identify optimal practice.
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Affiliation(s)
- K K Chau
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - L Barker
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - E P Budgell
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - K D Vihta
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - N Sims
- Department of Chemistry, Faculty of Science, University of Bath, Bath BA2 7AY, United Kingdom.
| | - B Kasprzyk-Hordern
- Department of Chemistry, Faculty of Science, University of Bath, Bath BA2 7AY, United Kingdom.
| | - E Harriss
- Bodleian Healthcare Libraries, University of Oxford, Oxford OX3 9DU, United Kingdom.
| | - D W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - D S Read
- UK Centre for Ecology & Hydrology, Wallingford OX10 8BB, United Kingdom.
| | - A S Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford OX4 2PG, United Kingdom.
| | - N Stoesser
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
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15
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Calero-Cáceres W, Tadesse D, Jaramillo K, Villavicencio X, Mero E, Lalaleo L, Welsh C, Villacís JE, Quentin E, Parra H, Ramirez MS, Harries AD, Balcázar JL. Characterization of the genetic structure of mcr-1 gene among Escherichia coli isolates recovered from surface waters and sediments from Ecuador. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150566. [PMID: 34582864 DOI: 10.1016/j.scitotenv.2021.150566] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/02/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Although anthropogenic activities contribute to the selection and spread of antibiotic resistance in aquatic environments, limited information is available from countries with absent or incomplete sewage treatment systems and the impact of their discharges onto water bodies. This study therefore aimed to characterize the genetic structure of colistin resistance (mcr) genes among Escherichia coli isolates recovered from surface waters and sediments in Ecuador. Out of 459 isolates, four Escherichia coli showed multidrug-resistant phenotypes, which harbored the mcr-1 gene and β-lactamases, such as blaTEM, blaCTX-M-15, blaCTX-M-55, or blaCTX-M-65 genes. Three E. coli isolates (U20, U30 and U144) shared a similar genetic environment surrounding the mcr-1 gene, which was located on plasmids. Only one E. coli isolate (U175) showed that the mcr-1 gene was chromosomally located. Moreover, the core genome multilocus sequence typing (cgMLST) analysis revealed that these isolates belong to different lineages. This study represents the first detection of the mcr-1 gene in multidrug-resistant E. coli isolates from environmental samples in Ecuador.
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Affiliation(s)
- William Calero-Cáceres
- UTA-RAM-One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador; Centro de Investigaciones Agropecuarias, Facultad de Ciencias Agropecuarias, Universidad Técnica de Ambato, Cevallos, Ecuador.
| | - Daniel Tadesse
- U.S. Food & Drug Administration, Center for Veterinary Medicine, Office of Research Laurel, MD 20708, USA
| | - Katherine Jaramillo
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos RAM, Instituto Nacional de Investigación en Salud Pública "Dr. Leopoldo Izquieta Pérez" INSPI, Quito, Ecuador
| | - Xavier Villavicencio
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos RAM, Instituto Nacional de Investigación en Salud Pública "Dr. Leopoldo Izquieta Pérez" INSPI, Quito, Ecuador
| | - Efraín Mero
- Centro de Investigaciones Agropecuarias, Facultad de Ciencias Agropecuarias, Universidad Técnica de Ambato, Cevallos, Ecuador
| | - Liliana Lalaleo
- UTA-RAM-One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador
| | - Caitlin Welsh
- U.S. Food & Drug Administration, Center for Veterinary Medicine, Office of Research Laurel, MD 20708, USA
| | - José E Villacís
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos RAM, Instituto Nacional de Investigación en Salud Pública "Dr. Leopoldo Izquieta Pérez" INSPI, Quito, Ecuador
| | - Emmanuelle Quentin
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos RAM, Instituto Nacional de Investigación en Salud Pública "Dr. Leopoldo Izquieta Pérez" INSPI, Quito, Ecuador
| | - Henry Parra
- Centro de Investigación Microbiológica Dr. Henry Parra, Guayaquil, Ecuador
| | - Maria Soledad Ramirez
- Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Anthony D Harries
- International Union Against Tuberculosis and Lung Disease, Paris, France; London School of Hygiene and Tropical Medicine, London, UK
| | - José L Balcázar
- Catalan Institute for Water Research (ICRA), 17003 Girona, Spain; University of Girona, 17004 Girona, Spain
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16
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Mahdavi S, Sadeghi M, Shokri R, Sadegh B. The Role of Bacteriophages as Important Reservoirs of Extended-Spectrum Beta-Lactamase Genes in Azerbaijan Hospitals. Microb Drug Resist 2022; 28:436-443. [PMID: 35076323 DOI: 10.1089/mdr.2021.0163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aims: The aim of this study was to investigate the role of resident bacteriophages in hospital effluents, as a potential reservoir of extended-spectrum beta-lactamase (ESBL) genes. Methods: Effluent samples were collected from four major medical centers in Azerbaijan. Phage enrichments were prepared and purified using standard subculturing, amplification, and phage purification protocols. DNA materials from phage stocks and bacterial isolates were examined for the presence of ESBL genes using polymerase chain reaction. Restriction fragment length polymorphism (RFLP) profiles were used for the construction of a dendrogram and cluster analysis. Results: A total of 112 phage enrichments were obtained from 48 effluent samples against resident bacterial hosts. A total of 95 nonduplicate Gram-negative isolates were recovered from effluent samples. The most common isolate was Escherichia coli (n = 48), followed by Klebsiella pneumoniae (n = 18), Pseudomonas spp. (n = 9), and Enterobacter cloacae (n = 6). Thirty-two EcoRV-RFLP profiles consisting of ∼4 to 20 bands were obtained for the 40 E. coli phage enrichments. ESBL genes were detected in 23 of 40 (57.5%) E. coli phage enrichments, including blaCTX-M (n = 15), blaTEM (n = 14), and blaSHV (n = 6). Detected genes in phage enrichments against resident hosts other than E. coli include blaTEM (n = 4), blaCTX-M (n = 3), and blaSHV (n = 1). A total of 63 (66.3%) bacterial isolates were positive for tested genes, including blaCTX-M (n = 32), blaTEM (n = 61), and blaSHV (n = 12). The present research provides a strong evidence for the possible role of bacteriophages in antimicrobial resistance genes circulation in Azerbaijan clinical settings through generalized transduction. Conclusions: Our results showed a remarkable occurrence of ESBL genes in bacteriophage and bacterial population of effluent discharge, which clearly indicates that bacteriophages are an important factor in ESBL genes exchange among bacterial population through generalized transduction.
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Affiliation(s)
- Sahar Mahdavi
- Department of Microbiology, Zanjan Branch, Islamic Azad University, Zanjan, Iran
| | - Mohammadreza Sadeghi
- Department of Clinical Microbiology, Maku Branch, Islamic Azad University, Maku, Iran.,Department of Clinical Microbiology, Faculty of Medical Sciences, Urmia Branch, Islamic Azad University, Urmia, Iran
| | - Rasoul Shokri
- Department of Microbiology, Zanjan Branch, Islamic Azad University, Zanjan, Iran
| | - Babak Sadegh
- Department of Clinical Microbiology, Faculty of Medical Sciences, Urmia Branch, Islamic Azad University, Urmia, Iran
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17
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Baghal Asghari F, Dehghani MH, Dehghanzadeh R, Farajzadeh D, Shanehbandi D, Mahvi AH, Yaghmaeian K, Rajabi A. Performance evaluation of ozonation for removal of antibiotic-resistant Escherichia coli and Pseudomonas aeruginosa and genes from hospital wastewater. Sci Rep 2021; 11:24519. [PMID: 34972828 PMCID: PMC8720092 DOI: 10.1038/s41598-021-04254-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/20/2021] [Indexed: 02/06/2023] Open
Abstract
The performance of ozonation for the removal of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) using Escherichia coli and Pseudomonas aeruginosa carrying ARGs from hospital wastewaters was evaluated in this study. Bacterial inactivation was determined using plate count methods and real time PCR for ARG damage (Sul1, blatem, blactx, blavim and qnrS). The reduction rate of bacterial cells and ARGs was increased by different amounts of transferred ozone dose from 11 to 45 mg/L. The concentration of 108 cfu/ml bacteria was reduced to an acceptable level by ozone treatment after a 5 min contact time, Although the removal rate was much higher for concentrations of 106 cfu/ml and 104 cfu/ml bacteria. Overall, the tendency of gene reduction by ozonation from more to less was 16S rRNA > sul1 > blatem > blactx > qnrS > blavim. Given that plasmid-borne ARGs can potentially be transferred to other bacteria even after the disinfection process, our results can provide important insights into the fate of ARGs during hospital wastewater ozonation.
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Affiliation(s)
- Farzaneh Baghal Asghari
- grid.411705.60000 0001 0166 0922Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hadi Dehghani
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran. .,Institute for Environmental Research, Center for Solid Waste Research, Tehran University of Medical Sciences, Tehran, Iran. .,Institute for Environmental Research, Center for Water Quality Research, Tehran University of Medical Sciences, Tehran, Iran.
| | - Reza Dehghanzadeh
- Health and Environment Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Davoud Farajzadeh
- grid.411468.e0000 0004 0417 5692Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Dariush Shanehbandi
- grid.412888.f0000 0001 2174 8913Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Hossein Mahvi
- grid.411705.60000 0001 0166 0922Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran ,grid.411705.60000 0001 0166 0922Institute for Environmental Research, Center for Solid Waste Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamyar Yaghmaeian
- grid.411705.60000 0001 0166 0922Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Akbar Rajabi
- grid.412888.f0000 0001 2174 8913 Health and Environment Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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18
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Göller PC, Elsener T, Lorgé D, Radulovic N, Bernardi V, Naumann A, Amri N, Khatchatourova E, Coutinho FH, Loessner MJ, Gómez-Sanz E. Multi-species host range of staphylococcal phages isolated from wastewater. Nat Commun 2021; 12:6965. [PMID: 34845206 PMCID: PMC8629997 DOI: 10.1038/s41467-021-27037-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/21/2021] [Indexed: 12/19/2022] Open
Abstract
The host range of bacteriophages defines their impact on bacterial communities and genome diversity. Here, we characterize 94 novel staphylococcal phages from wastewater and establish their host range on a diversified panel of 117 staphylococci from 29 species. Using this high-resolution phage-bacteria interaction matrix, we unveil a multi-species host range as a dominant trait of the isolated staphylococcal phages. Phage genome sequencing shows this pattern to prevail irrespective of taxonomy. Network analysis between phage-infected bacteria reveals that hosts from multiple species, ecosystems, and drug-resistance phenotypes share numerous phages. Lastly, we show that phages throughout this network can package foreign genetic material enclosing an antibiotic resistance marker at various frequencies. Our findings indicate a weak host specialism of the tested phages, and therefore their potential to promote horizontal gene transfer in this environment.
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Affiliation(s)
- Pauline C. Göller
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Tabea Elsener
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Dominic Lorgé
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Natasa Radulovic
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Viona Bernardi
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Annika Naumann
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Nesrine Amri
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Ekaterina Khatchatourova
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Felipe Hernandes Coutinho
- grid.26811.3c0000 0001 0586 4893Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Martin J. Loessner
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Elena Gómez-Sanz
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland. .,Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain.
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19
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Distribution of Antimicrobial Resistance and Virulence Genes within the Prophage-Associated Regions in Nosocomial Pathogens. mSphere 2021; 6:e0045221. [PMID: 34232073 PMCID: PMC8386436 DOI: 10.1128/msphere.00452-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Prophages are often involved in host survival strategies and contribute toward increasing the genetic diversity of the host genome. Prophages also drive horizontal propagation of various genes as vehicles. However, there are few retrospective studies contributing to the propagation of antimicrobial resistance (AMR) and virulence factor (VF) genes by prophage. We extracted the complete genome sequences of seven pathogens, including ESKAPE bacteria and Escherichia coli from a public database, and examined the distribution of both the AMR and VF genes in prophage-like regions. We found that the ratios of AMR and VF genes greatly varied among the seven species. More than 70% of Enterobacter cloacae strains had VF genes, but only 1.2% of Klebsiella pneumoniae strains had VF genes from prophages. AMR and VF genes are unlikely to exist together in the same prophage region except in E. coli and Staphylococcus aureus, and the distribution patterns of prophage types containing AMR genes are distinct from those of VF gene-carrying prophage types. AMR genes in the prophage were located near transposase and/or integrase. The prophage containing class 1 integrase possessed a significantly greater number of AMR genes than did prophages with no class 1 integrase. The results of this study present a comprehensive picture of AMR and VF genes present within, or close to, prophage-like elements and different prophage patterns between AMR- or VF-encoding prophage-like elements. IMPORTANCE Although we believe phages play an important role in horizontal gene transfer in exchanging genetic material, we do not know the distribution of the antimicrobial resistance (AMR) and/or virulence factor (VF) genes in prophages. We collected different prophage elements from the complete genome sequences of seven species—Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae, and Escherichia coli—and characterized the distribution of antimicrobial resistance and virulence genes located in the prophage region. While virulence genes in prophage were species specific, antimicrobial resistance genes in prophages were highly conserved in various species. An integron structure was detected within specific prophage regions such as P1-like prophage element. Maximum of 10 antimicrobial resistance genes were found in a single prophage region, suggesting that prophages act as a reservoir for antimicrobial resistance genes. The results of this study show the different characteristic structures between AMR- or VF-encoding prophages.
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Koutsoumanis K, Allende A, Álvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Argüello H, Berendonk T, Cavaco LM, Gaze W, Schmitt H, Topp E, Guerra B, Liébana E, Stella P, Peixe L. Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain. EFSA J 2021; 19:e06651. [PMID: 34178158 PMCID: PMC8210462 DOI: 10.2903/j.efsa.2021.6651] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.
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21
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Diversity of β-lactamase-encoding genes in wastewater: bacteriophages as reporters. Arch Virol 2021; 166:1337-1344. [PMID: 33683473 DOI: 10.1007/s00705-021-05024-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
A reservoir of antibiotic resistance genes (ARGs) is present in pathogenic, commensal, and environmental bacteria as well as in mobile genetic elements, including bacteriophages. Wastewater treatment plants (WWTPs) are considered hotspots for the spread of ARGs. The aim of this work was to analyze the diversity of the highly prevalent ARGs blaCTX-M and blaTEM in bacterial and bacteriophage fractions associated with human and animal environments through the study of urban waste and animal residues discharged into WWTPs to provide information about the composition and maintenance of the current resistome in Buenos Aires, Argentina. The results showed that a putative extended-spectrum variant of the blaTEM gene was the most frequently detected, with blaTEM-116 being the most prevalent, while a recently described type, blaTEM-229, was also found. In the bacteriophage fraction, we detected blaCTX-M genes from four out of the five clusters described. The detection of blaCTX- M-9-like and blaCTX-M-25-like genes was unexpected based on surveys of the ARGs from clinical pathogens circulating regionally. The finding of divergent blaCTX-M sequences associated with previously reported environmental genes argues in favor of the natural environment as a reservoir of resistance genes. ARGs were detected in bacteriophages as frequently as in bacterial communities, and furthermore, the blaCTX-M genes were more diverse in the bacteriophage fraction. Bacteriophages might therefore play a role in the spread of ARGs in the environment, but they might also be used as "reporters" for monitoring circulating ARGs.
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22
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Meng T, Cheng W, Wan T, Wang M, Ren J, Li Y, Huang C. Occurrence of antibiotics in rural drinking water and related human health risk assessment. ENVIRONMENTAL TECHNOLOGY 2021; 42:671-681. [PMID: 31290372 DOI: 10.1080/09593330.2019.1642390] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/05/2019] [Indexed: 06/09/2023]
Abstract
Antibiotic residues in drinking water can have a negative impact on both human and environmental health. However, drinking water purification processes employed in rural areas are often less complicated than those used in urban areas. The occurrence of antibiotic residues in rural drinking water and their potential effects on residents' health remains to be established. In this study, we measured antibiotic levels in rural drinking water using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), and evaluated the associated health risks based on Chinese population exposure parameters. Twenty-three antibiotics were detected in drinking water samples, of which fluoroquinolones and macrolides were the most common. The type and concentration of antibiotics in drinking water were affected both by the quality of the water source and by the water purification process used. The health risks associated with antibiotics in drinking water were within acceptable levels and likely to have little impact on human health. Of the antibiotics detected, salinomycin presented the greatest risk to human health. These findings can help to play a role in devising strategies to ensure drinking water safety.
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Affiliation(s)
- Ting Meng
- State Key Laboratory of Eco-Hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Wen Cheng
- State Key Laboratory of Eco-Hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Tian Wan
- State Key Laboratory of Eco-Hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Min Wang
- State Key Laboratory of Eco-Hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Jiehui Ren
- State Key Laboratory of Eco-Hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Yikun Li
- State Key Laboratory of Eco-Hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, People's Republic of China
| | - Chen Huang
- State Key Laboratory of Eco-Hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, People's Republic of China
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23
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Talavera-González JM, Talavera-Rojas M, Soriano-Vargas E, Vázquez-Navarrete J, Salgado-Miranda C. In vitro transduction of antimicrobial resistance genes into Escherichia coli isolates from backyard poultry in Mexico. Can J Microbiol 2021; 67:415-425. [PMID: 33395360 DOI: 10.1139/cjm-2020-0280] [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: 01/23/2023]
Abstract
The transmission of multidrug-resistant pathogens and antimicrobial resistance genes is an emerging problem involving multiple factors (humans, domestic animals, wildlife). The aim of this study was to investigate the presence of Escherichia coli isolates with different antimicrobial resistance genes from backyard poultry and to demonstrate the in vitro transduction phenomenon of these genes between phages from migratory wild birds and poultry E. coli isolates. We collected 197 E. coli isolates from chickens, turkeys, and ducks in backyard production units (northern region of the State of Mexico). Isolates were resistant to ampicillin (80.7%), tetracycline (64.4%), carbenicillin (56.3%), and nalidixic acid and trimethoprim-sulfamethoxazole (both, 26.9%). Moreover, the genes blaTEM (56.3%), tetB (20.8%), tetA (19.2%), sulI (7.6%), sulII (10.1%), qnrA (9.6%), and qnrB (5.5%) were found. In vitro transduction using phages from migratory wild birds sampled in the wetland Chimaliapan (State of Mexico) was successfully achieved. It was possible to transduce qnrA, tetB, blaTEM, and sulII genes to E. coli isolates from poultry. This is the first report that describes the transduction of antimicrobial resistance genes from phages of migratory wild birds to poultry and suggests the possible transmission in backyard production units.
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Affiliation(s)
- Juan Martín Talavera-González
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco, Km 15.5, Toluca, Estado de México 50200, México
| | - Martín Talavera-Rojas
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco, Km 15.5, Toluca, Estado de México 50200, México
| | - Edgardo Soriano-Vargas
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco, Km 15.5, Toluca, Estado de México 50200, México
| | - Jesús Vázquez-Navarrete
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Carretera México-Toluca Km. 15.5, Ciudad de México, México
| | - Celene Salgado-Miranda
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco, Km 15.5, Toluca, Estado de México 50200, México
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24
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Abe K, Nomura N, Suzuki S. Biofilms: hot spots of horizontal gene transfer (HGT) in aquatic environments, with a focus on a new HGT mechanism. FEMS Microbiol Ecol 2020; 96:5766226. [PMID: 32109282 PMCID: PMC7189800 DOI: 10.1093/femsec/fiaa031] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/27/2020] [Indexed: 12/21/2022] Open
Abstract
Biofilms in water environments are thought to be hot spots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). ARGs can be spread via HGT, though mechanisms are known and have been shown to depend on the environment, bacterial communities and mobile genetic elements. Classically, HGT mechanisms include conjugation, transformation and transduction; more recently, membrane vesicles (MVs) have been reported as DNA reservoirs implicated in interspecies HGT. Here, we review the current knowledge on the HGT mechanisms with a focus on the role of MVs and the methodological innovations in the HGT research.
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Affiliation(s)
- Kimihiro Abe
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8577 Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8577 Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, 305-8577 Japan
| | - Satoru Suzuki
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577 Japan
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25
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Rodríguez-Rubio L, Serna C, Ares-Arroyo M, Matamoros BR, Delgado-Blas JF, Montero N, Bernabe-Balas C, Wedel EF, Mendez IS, Muniesa M, Gonzalez-Zorn B. Extensive antimicrobial resistance mobilization via multicopy plasmid encapsidation mediated by temperate phages. J Antimicrob Chemother 2020; 75:3173-3180. [PMID: 32719862 PMCID: PMC7566468 DOI: 10.1093/jac/dkaa311] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 06/09/2020] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES To investigate the relevance of multicopy plasmids in antimicrobial resistance and assess their mobilization mediated by phage particles. METHODS Several databases with complete sequences of plasmids and annotated genes were analysed. The 16S methyltransferase gene armA conferring high-level aminoglycoside resistance was used as a marker in eight different plasmids, from different incompatibility groups, and with differing sizes and plasmid copy numbers. All plasmids were transformed into Escherichia coli bearing one of four different lysogenic phages. Upon induction, encapsidation of armA in phage particles was evaluated using qRT-PCR and Southern blotting. RESULTS Multicopy plasmids carry a vast set of emerging clinically important antimicrobial resistance genes. However, 60% of these plasmids do not bear mobility (MOB) genes. When carried on these multicopy plasmids, mobilization of a marker gene armA into phage capsids was up to 10000 times more frequent than when it was encoded by a large plasmid with a low copy number. CONCLUSIONS Multicopy plasmids and phages, two major mobile genetic elements (MGE) in bacteria, represent a novel high-efficiency transmission route of antimicrobial resistance genes that deserves further investigation.
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Affiliation(s)
- Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Carlos Serna
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Manuel Ares-Arroyo
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Bosco R Matamoros
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Jose F Delgado-Blas
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Natalia Montero
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Cristina Bernabe-Balas
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Emilia F Wedel
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Irene S Mendez
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Bruno Gonzalez-Zorn
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
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26
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Evolution of antibiotic resistance at low antibiotic concentrations including selection below the minimal selective concentration. Commun Biol 2020; 3:467. [PMID: 32884065 PMCID: PMC7471295 DOI: 10.1038/s42003-020-01176-w] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 07/24/2020] [Indexed: 12/15/2022] Open
Abstract
Determining the selective potential of antibiotics at environmental concentrations is critical for designing effective strategies to limit selection for antibiotic resistance. This study determined the minimal selective concentrations (MSCs) for macrolide and fluoroquinolone antibiotics included on the European Commissionʼs Water Framework Directive’s priority hazardous substances Watch List. The macrolides demonstrated positive selection for ermF at concentrations 1–2 orders of magnitude greater (>500 and <750 µg/L) than measured environmental concentrations (MECs). Ciprofloxacin illustrated positive selection for intI1 at concentrations similar to current MECs (>7.8 and <15.6 µg/L). This highlights the need for compound specific assessment of selective potential. In addition, a sub-MSC selective window defined by the minimal increased persistence concentration (MIPC) is described. Differential rates of negative selection (or persistence) were associated with elevated prevalence relative to the no antibiotic control below the MSC. This increased persistence leads to opportunities for further selection over time and risk of human exposure and environmental transmission. Stanton et al. determine the minimal selective concentrations for macrolide and fluoroquinolone antibiotics and describe a selective window defined by the minimal increased persistence concentration. These assessments and thresholds allow for better assessment of potential selection for antibiotic resistance and the risks of human exposure and environmental transmission.
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27
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Blanco-Picazo P, Roscales G, Toribio-Avedillo D, Gómez-Gómez C, Avila C, Ballesté E, Muniesa M, Rodríguez-Rubio L. Antibiotic Resistance Genes in Phage Particles from Antarctic and Mediterranean Seawater Ecosystems. Microorganisms 2020; 8:microorganisms8091293. [PMID: 32847015 PMCID: PMC7565065 DOI: 10.3390/microorganisms8091293] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 01/17/2023] Open
Abstract
Anthropogenic activities are a key factor in the development of antibiotic resistance in bacteria, a growing problem worldwide. Nevertheless, antibiotics and resistances were being generated by bacterial communities long before their discovery by humankind, and might occur in areas without human influence. Bacteriophages are known to play a relevant role in the dissemination of antibiotic resistance genes (ARGs) in aquatic environments. In this study, five ARGs (blaTEM, blaCTX-M-1, blaCTX-M-9, sul1 and tetW) were monitored in phage particles isolated from seawater of two different locations: (i) the Mediterranean coast, subjected to high anthropogenic pressure, and (ii) the Antarctic coast, where the anthropogenic impact is low. Although found in lower quantities, ARG-containing phage particles were more prevalent among the Antarctic than the Mediterranean seawater samples and Antarctic bacterial communities were confirmed as their source. In the Mediterranean area, ARG-containing phages from anthropogenic fecal pollution might allow ARG transmission through the food chain. ARGs were detected in phage particles isolated from fish (Mediterranean, Atlantic, farmed, and frozen), the most abundant being β-lactamases. Some of these particles were infectious in cultures of the fecal bacteria Escherichia coli. By serving as ARG reservoirs in marine environments, including those with low human activity, such as the Antarctic, phages could contribute to ARG transmission between bacterial communities.
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Affiliation(s)
- Pedro Blanco-Picazo
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain; (P.B.-P.); (G.R.); (D.T.-A.); (C.G.-G.); (E.B.)
| | - Gabriel Roscales
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain; (P.B.-P.); (G.R.); (D.T.-A.); (C.G.-G.); (E.B.)
| | - Daniel Toribio-Avedillo
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain; (P.B.-P.); (G.R.); (D.T.-A.); (C.G.-G.); (E.B.)
| | - Clara Gómez-Gómez
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain; (P.B.-P.); (G.R.); (D.T.-A.); (C.G.-G.); (E.B.)
| | - Conxita Avila
- Department of Evolutionary Biology, Ecology and Environmental Sciences (BEECA), Faculty of Biology, and Biodiversity Research Institute (IrBIO), University of Barcelona, Diagonal 643, 08028 Barcelona, Spain;
| | - Elisenda Ballesté
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain; (P.B.-P.); (G.R.); (D.T.-A.); (C.G.-G.); (E.B.)
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain; (P.B.-P.); (G.R.); (D.T.-A.); (C.G.-G.); (E.B.)
- Correspondence: (M.M.); (L.R.-R.)
| | - Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain; (P.B.-P.); (G.R.); (D.T.-A.); (C.G.-G.); (E.B.)
- Correspondence: (M.M.); (L.R.-R.)
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28
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Correlation between Exogenous Compounds and the Horizontal Transfer of Plasmid-Borne Antibiotic Resistance Genes. Microorganisms 2020; 8:microorganisms8081211. [PMID: 32784449 PMCID: PMC7463591 DOI: 10.3390/microorganisms8081211] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/03/2020] [Accepted: 08/07/2020] [Indexed: 12/31/2022] Open
Abstract
The global spread of antibiotic resistance has posed a serious threat to public healthcare and undermined decades of progress made in the fight against bacterial infections. It has been demonstrated that the lack of novel effective antibiotics and rapid spread of antibiotic resistance genes via horizontal transfer in the ecosystem are mainly responsible for this crisis. Notably, plasmid-mediated horizontal transfer of antibiotic resistance genes (ARGs) is recognized as the most dominant dissemination pathway of ARGs in humans, animals and environmental settings. Antibiotic selective pressure has always been regarded as one of the crucial contributors to promoting the dissemination of antibiotic resistance through horizontal gene transfer (HGT). However, the roles of exogenous compounds and particularly non-antibiotic drugs in the spread of ARGs are still underappreciated. In this review, we first summarize the major pathways of HGT in bacteria, including conjugation, transformation, transduction and vesiduction. Subsequently, an overview of these compounds capable of promoting the HGT is presented, which guides to the formulation of more reasonable dosing regimens and drug residue standards in clinical practice. By contrast, these compounds that display an inhibition effect on HGT are also highlighted, which provides a unique strategy to minimize the spread of ARGs. Lastly, we discuss the implementations and challenges in bringing these HGT inhibitors into clinical trials.
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29
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Blanco-Picazo P, Fernández-Orth D, Brown-Jaque M, Miró E, Espinal P, Rodríguez-Rubio L, Muniesa M, Navarro F. Unravelling the consequences of the bacteriophages in human samples. Sci Rep 2020; 10:6737. [PMID: 32317653 PMCID: PMC7174282 DOI: 10.1038/s41598-020-63432-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/31/2020] [Indexed: 12/26/2022] Open
Abstract
Bacteriophages are abundant in human biomes and therefore in human clinical samples. Although this is usually not considered, they might interfere with the recovery of bacterial pathogens at two levels: 1) by propagating in the enrichment cultures used to isolate the infectious agent, causing the lysis of the bacterial host and 2) by the detection of bacterial genes inside the phage capsids that mislead the presence of the bacterial pathogen. To unravel these interferences, human samples (n = 271) were analyzed and infectious phages were observed in 11% of blood culture, 28% of serum, 45% of ascitic fluid, 14% of cerebrospinal fluid and 23% of urine samples. The genetic content of phage particles from a pool of urine and ascitic fluid samples corresponded to bacteriophages infecting different bacterial genera. In addition, many bacterial genes packaged in the phage capsids, including antibiotic resistance genes and 16S rRNA genes, were detected in the viromes. Phage interference can be minimized applying a simple procedure that reduced the content of phages up to 3 logs while maintaining the bacterial load. This method reduced the detection of phage genes avoiding the interference with molecular detection of bacteria and reduced the phage propagation in the cultures, enhancing the recovery of bacteria up to 6 logs.
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Affiliation(s)
- Pedro Blanco-Picazo
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028, Barcelona, Spain
| | - Dietmar Fernández-Orth
- European Genome-phenome Archive, Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Maryury Brown-Jaque
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028, Barcelona, Spain
| | - Elisenda Miró
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041, Barcelona, Spain
| | - Paula Espinal
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041, Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028, Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028, Barcelona, Spain.
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041, Barcelona, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
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30
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Fiorentino A, Esteban B, Garrido-Cardenas JA, Kowalska K, Rizzo L, Aguera A, Pérez JAS. Effect of solar photo-Fenton process in raceway pond reactors at neutral pH on antibiotic resistance determinants in secondary treated urban wastewater. JOURNAL OF HAZARDOUS MATERIALS 2019; 378:120737. [PMID: 31202058 DOI: 10.1016/j.jhazmat.2019.06.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 05/20/2023]
Abstract
Solar photo-Fenton process in raceway pond reactors was investigated at neutral pH as a sustainable tertiary treatment of real urban wastewater. In particular, the effect on antibiotic resistance determinants was evaluated. An effective inactivation of different wild bacterial populations was achieved considering total and cefotaxime resistant bacteria. The detection limit (1 CFU mL-1) was achieved in the range 80-100 min (5.4-6.7 kJ L-1 of cumulative solar energy required) for Total Coliforms (TC) (40-60 min for resistant TC, 4.3-5.2 kJ L-1), 60-80 min (4.5-5.4 kJ L-1) for Escherichia coli (E. coli) (40 min for resistant E. coli, 4.1-4.7 kJ L-1) and 40-60 min (3.9-4.5 kJ L-1) for Enterococcus sp. (Entero) (30-40 min for resistant Entero, 3.2-3.8 kJ L-1) with 20 mg L-1 Fe2+ and 50 mg L-1 H2O2. Under these mild oxidation conditions, 7 out of the 10 detected antibiotics were effectively removed (60-100%). As the removal of antibiotic resistance genes (ARGs) is of concern, no conclusive results were obtained, as sulfonamide resistance gene was reduced to some extent (relative abundance <1), meanwhile class 1 integron intI1 and ß-lactam resistance genes were not affected. Accordingly, more research and likely more intensive oxidative conditions are needed for an efficient ARGs removal.
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Affiliation(s)
- Antonino Fiorentino
- Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, SA, Italy
| | - Belén Esteban
- Department of Chemical Engineering, Universitiy of Almeria, Ctra. Sacramento s/n, ES04120, Almería, Spain; Solar Energy Research Center (CIESOL), Ctra. Sacramento s/n, ES04120, Almería, Spain
| | | | - Katarzyna Kowalska
- Silesian University of Technology, Faculty of Energy and Environmental Engineering, Environmental Biotechnology Department, ul. Akademicka 2, 44-100, Gliwice, Poland; Silesian University of Technology, The Biotechnology Centre, ul. B. Krzywoustego 8, 44-100, Gliwice, Poland
| | - Luigi Rizzo
- Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, SA, Italy.
| | - Ana Aguera
- Solar Energy Research Center (CIESOL), Ctra. Sacramento s/n, ES04120, Almería, Spain.
| | - José Antonio Sánchez Pérez
- Department of Chemical Engineering, Universitiy of Almeria, Ctra. Sacramento s/n, ES04120, Almería, Spain
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31
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Infectious phage particles packaging antibiotic resistance genes found in meat products and chicken feces. Sci Rep 2019; 9:13281. [PMID: 31527758 PMCID: PMC6746790 DOI: 10.1038/s41598-019-49898-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/29/2019] [Indexed: 11/08/2022] Open
Abstract
Bacteriophages can package part of their host's genetic material, including antibiotic resistance genes (ARGs), contributing to a rapid dissemination of resistances among bacteria. Phage particles containing ARGs were evaluated in meat, pork, beef and chicken minced meat, and ham and mortadella, purchased in local retailer. Ten ARGs (blaTEM, blaCTX-M-1, blaCTX-M-9, blaOXA-48, blaVIM, qnrA, qnrS, mecA, armA and sul1) were analyzed by qPCR in the phage DNA fraction. The genes were quantified, before and after propagation experiments in Escherichia coli, to evaluate the ability of ARG-carrying phage particles to infect and propagate in a bacterial host. According to microbiological parameters, all samples were acceptable for consumption. ARGs were detected in most of the samples after particle propagation indicating that at least part of the isolated phage particles were infectious, being sul1the most abundant ARG in all the matrices followed by β-lactamase genes. ARGs were also found in the phage DNA fraction of thirty-seven archive chicken cecal samples, confirming chicken fecal microbiota as an important ARG reservoir and the plausible origin of the particles found in meat. Phages are vehicles for gene transmission in meat that should not be underestimated as a risk factor in the global crisis of antibiotic resistance.
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Zhang A, Call DR, Besser TE, Liu J, Jones L, Wang H, Davis MA. β-lactam resistance genes in bacteriophage and bacterial DNA from wastewater, river water, and irrigation water in Washington State. WATER RESEARCH 2019; 161:335-340. [PMID: 31212239 DOI: 10.1016/j.watres.2019.06.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 05/04/2023]
Abstract
Our objective was to determine whether β-lactamase genes are carried within bacteriophage capsids, as a first step towards exploring the possible role of bacteriophages as vehicles for dispersal of antimicrobial resistance genes through an agricultural region of Washington State. Water samples (n = 178) from municipal wastewater treatment plants, river and irrigation canals were collected over a period of eight months. The occurrence of four β-lactam resistance gene groups (blaTEM, blaCTX-M, blaPSE and blaCMY-2) and three carbapenem resistance genes (blaKPC, blaOXA-48-like, and blaNDM) in bacterial and phage fractions of water samples was evaluated by PCR. All of the seven targeted resistance genes were detected both in wastewater and river water samples. Relatively high proportions of samples (7.3%-64.9%) positive for resistance genes were found in bacteriophage fractions of water samples compared to the bacterial fractions (5.4%-36.8%). blaOXA-48-like (57.3%) and blaTEM (64.0%) were the most prevalent antimicrobial resistance genes detected at all the sampling points. Resistance genes are commonly present in treated wastewater flowing through municipal and agricultural environments, indicating a plausible role for this water in the dissemination of antimicrobial resistance traits, including blaCTX-M.
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Affiliation(s)
- Anyun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China; Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Douglas R Call
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Thomas E Besser
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, USA; Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Jinxin Liu
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, USA; Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Lisa Jones
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Hongning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Margaret A Davis
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, USA.
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33
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Calero-Cáceres W, Ye M, Balcázar JL. Bacteriophages as Environmental Reservoirs of Antibiotic Resistance. Trends Microbiol 2019; 27:570-577. [PMID: 30905524 DOI: 10.1016/j.tim.2019.02.008] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/07/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023]
Abstract
Although antibiotic resistance represents a significant and growing public health concern, the contribution of bacteriophages (phages) to the mobilization of antibiotic resistance genes (ARGs) in the environment has not been extensively studied. Recent studies, however, suggest that phages play an important role in the acquisition, maintenance, and spread of ARGs than previously expected. This Opinion article offers an update on the contribution of phages to environmental antibiotic resistance. A better understanding of the mechanisms and factors that promote antibiotic resistance may significantly contribute to the implementation of control strategies.
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Affiliation(s)
- William Calero-Cáceres
- UTA-RAM-OneHealth Group, Centro de Investigaciones Agropecuarias, Facultad de Ciencias Agropecuarias, Universidad Técnica de Ambato, Tungurahua, Ecuador
| | - Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona 17003, Spain.
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Calero-Cáceres W, Balcázar JL. Antibiotic resistance genes in bacteriophages from diverse marine habitats. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:452-455. [PMID: 30447583 DOI: 10.1016/j.scitotenv.2018.11.166] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/18/2018] [Accepted: 11/11/2018] [Indexed: 06/09/2023]
Abstract
Although antibiotic resistance represents a significant and growing threat to human and environmental health worldwide, the contribution of bacteriophages (phages) to the acquisition and spread of antibiotic resistance genes (ARGs) in the environment has not been extensively explored. In this study, a comprehensive analysis of several viromes from diverse marine habitats was performed to investigate whether or not phages carry ARGs. The analysis provides strong evidence that phages from marine habitats are potential reservoirs of ARGs. In fact, genes conferring resistance to aminocoumarin, bacitracin and multidrug resistance (particularly the mexB gene) were found in all analyzed marine viromes. Given this, the role of phages as reservoirs of ARGs should not be underestimated considering their global distribution.
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Affiliation(s)
- William Calero-Cáceres
- UTA-RAM-OneHealth Group, Centro de Investigaciones Agropecuarias, Facultad de Ciencias Agropecuarias, Universidad Técnica de Ambato, Tungurahua, Ecuador
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), University of Girona, Girona, Spain.
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Fernández-Orth D, Miró E, Brown-Jaque M, Rodríguez-Rubio L, Espinal P, Rodriguez-Navarro J, González-López JJ, Muniesa M, Navarro F. Faecal phageome of healthy individuals: presence of antibiotic resistance genes and variations caused by ciprofloxacin treatment. J Antimicrob Chemother 2019; 74:854-864. [DOI: 10.1093/jac/dky540] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/19/2018] [Accepted: 11/26/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Elisenda Miró
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, Barcelona, Spain
| | - Maryury Brown-Jaque
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, Annex, Floor 0, Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, Annex, Floor 0, Barcelona, Spain
| | - Paula Espinal
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, Barcelona, Spain
| | - Judith Rodriguez-Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan José González-López
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Pg Vall d’Hebron 119-129, Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, Annex, Floor 0, Barcelona, Spain
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
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36
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Peterson E, Kaur P. Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens. Front Microbiol 2018; 9:2928. [PMID: 30555448 PMCID: PMC6283892 DOI: 10.3389/fmicb.2018.02928] [Citation(s) in RCA: 439] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 11/13/2022] Open
Abstract
Emergence of antibiotic resistant pathogenic bacteria poses a serious public health challenge worldwide. However, antibiotic resistance genes are not confined to the clinic; instead they are widely prevalent in different bacterial populations in the environment. Therefore, to understand development of antibiotic resistance in pathogens, we need to consider important reservoirs of resistance genes, which may include determinants that confer self-resistance in antibiotic producing soil bacteria and genes encoding intrinsic resistance mechanisms present in all or most non-producer environmental bacteria. While the presence of resistance determinants in soil and environmental bacteria does not pose a threat to human health, their mobilization to new hosts and their expression under different contexts, for example their transfer to plasmids and integrons in pathogenic bacteria, can translate into a problem of huge proportions, as discussed in this review. Selective pressure brought about by human activities further results in enrichment of such determinants in bacterial populations. Thus, there is an urgent need to understand distribution of resistance determinants in bacterial populations, elucidate resistance mechanisms, and determine environmental factors that promote their dissemination. This comprehensive review describes the major known self-resistance mechanisms found in producer soil bacteria of the genus Streptomyces and explores the relationships between resistance determinants found in producer soil bacteria, non-producer environmental bacteria, and clinical isolates. Specific examples highlighting potential pathways by which pathogenic clinical isolates might acquire these resistance determinants from soil and environmental bacteria are also discussed. Overall, this article provides a conceptual framework for understanding the complexity of the problem of emergence of antibiotic resistance in the clinic. Availability of such knowledge will allow researchers to build models for dissemination of resistance genes and for developing interventions to prevent recruitment of additional or novel genes into pathogens.
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Affiliation(s)
- Elizabeth Peterson
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, United States
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37
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Wang M, Xiong W, Liu P, Xie X, Zeng J, Sun Y, Zeng Z. Metagenomic Insights Into the Contribution of Phages to Antibiotic Resistance in Water Samples Related to Swine Feedlot Wastewater Treatment. Front Microbiol 2018; 9:2474. [PMID: 30459724 PMCID: PMC6232670 DOI: 10.3389/fmicb.2018.02474] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 09/27/2018] [Indexed: 12/21/2022] Open
Abstract
In this study, we examined the types of antibiotic resistance genes (ARGs) possessed by bacteria and bacteriophages in swine feedlot wastewater before and after treatment using a metagenomics approach. We found that the relative abundance of ARGs in bacterial DNA in all water samples was significantly higher than that in phages DNA (>10.6-fold), and wastewater treatment did not significantly change the relative abundance of bacterial- or phage-associated ARGs. We further detected the distribution and diversity of the different types of ARGs according to the class of antibiotics to which they confer resistance, the tetracycline resistance genes were the most abundant resistance genes and phages were more likely to harbor ATP-binding cassette transporter family and ribosomal protection genes. Moreover, the colistin resistance gene mcr-1 was also detected in the phage population. When assessing the contribution of phages in spreading different groups of ARGs, β-lactamase resistance genes had a relatively high spreading ability even though the abundance was low. These findings possibly indicated that phages not only could serve as important reservoir of ARG but also carry particular ARGs in swine feedlot wastewater, and this phenomenon is independent of the environment.
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Affiliation(s)
- Mianzhi Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wenguang Xiong
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Peng Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiying Xie
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jiaxiong Zeng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yongxue Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhenling Zeng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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38
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Wang Q, Zeng X, Yang Q, Yang C. Identification of a bacteriophage from an environmental multidrug-resistant E. coli isolate and its function in horizontal transfer of ARGs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 639:617-623. [PMID: 29803035 DOI: 10.1016/j.scitotenv.2018.05.213] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/08/2018] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
Horizontal transfer of ARGs was generally considered to be mediated by three methods - transformation, conjugation and transduction through phages - during which the contribution of bacteriophages to gene transfer in the environment is unclear or even questioned. In this study, a multiple-antibiotic-resistant Escherichia coli strain and its phage (YZ1) were isolated from a municipal wastewater treatment system. The results of the morphological and genomic analyses of phage YZ1 showed that it is a member of the T7 viral genus in the subfamily Autographivirinae. Its genome is similar to that of the E. coli phage K1F in both organization and sequence and does not encode ARGs. However, 28 paired reads in the raw sequencing data aligned to ARGs, including those promoting β-lactam, aminoglycoside, and fluoroquinolone resistance, among others. Quantitative PCR showed that ARGs were present in bacteriophage DNA (approximately 103 copies/mL) and were also detected in the bacterial host DNA. The results suggested that while infrequent, some ARG-carrying transducing phages were presumably generated by erroneous packaging during infection of antibiotic-resistant bacteria, which may create the possibility of horizontal transfer of ARGs.
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Affiliation(s)
- Qiang Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Key Laboratory for Microorganisms and Functional Molecules (Henan Normal University), University of Henan Province, Xinxiang 453007, China
| | - Xiangpeng Zeng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Qingxiang Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Key Laboratory for Microorganisms and Functional Molecules (Henan Normal University), University of Henan Province, Xinxiang 453007, China.
| | - Chuanzhen Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
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Zhou M, Zhu T, Fei X. Enhanced Adsorption Performance of Oxytetracycline by Desugared Reed Residues. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15102229. [PMID: 30314375 PMCID: PMC6210684 DOI: 10.3390/ijerph15102229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 11/20/2022]
Abstract
The performance of oxytetracycline adsorption by untreated reed roots, stems and leaves, as well as the desugared reed roots, stems and leaves, was investigated with scanning electron microscopy, Fourier-transform infrared spectroscopy, elemental analysis and surface area analysis to understand the adsorption mechanism. The results showed that the adsorption capacities of untreated reed were 416.35 mg/kg for roots, 341.92 mg/kg for stems and 280.21 mg/kg for leaves, and can be increased significantly by a factor of 8–12 after desugarization. The pseudo-first-order kinetic model was more suitable for describing the adsorption kinetics of reed residues, and the isothermal adsorption process was fitted well by both the Langmuir and Freundlich models. The thermodynamic process suggested that the adsorption was a spontaneous endothermic reaction, and mainly physical adsorption-dominated. The desugared reed tissues had a larger surface area and smaller pore area, and the aromaticity of reed residues increased; on the other hand, the polarity and hydrophilicity decreased after desugarization, thus revealing the mechanism of enhanced OTC(oxytetracycline) adsorption by desugared reed residues. This study suggests that the reed residues contribute the complex adsorption ability for both inorganic and organic contaminates. Corruption of the reed can enhance the adsorption; thus, protecting the natural reed residue and letting it naturally corrupt, rather than artificially cleaning it up, can effectively promote the adsorption of pollutants in the environment and protect environmental and public health.
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Affiliation(s)
- Min Zhou
- School of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
- Henan College of Transportation, Zhengzhou 450008, China.
| | - Tao Zhu
- Henan College of Transportation, Zhengzhou 450008, China.
| | - Xiaohua Fei
- Key Laboratory of Subsurface Hydrology and Ecology in Arid Areas, Ministry of Education, Chang'an University, Xi'an 710054, China.
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40
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The disparate effects of bacteriophages on antibiotic-resistant bacteria. Emerg Microbes Infect 2018; 7:168. [PMID: 30302018 PMCID: PMC6177407 DOI: 10.1038/s41426-018-0169-z] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 08/30/2018] [Accepted: 09/05/2018] [Indexed: 01/21/2023]
Abstract
Faced with the crisis of multidrug-resistant bacteria, bacteriophages, viruses that infect and replicate within bacteria, have been reported to have both beneficial and detrimental effects with respect to disease management. Bacteriophages (phages) have important ecological and evolutionary impacts on their bacterial hosts and have been associated with therapeutic use to kill bacterial pathogens, but can lead to the transmission of antibiotic resistance. Although the process known as transduction has been reported for many bacterial species by classic and modern genetic approaches, its contribution to the spread of antibiotic resistance in nature remains unclear. In addition, detailed molecular studies have identified phages residing in bacterial genomes, revealing unexpected interactions between phages and their bacterial hosts. Importantly, antibiotics can induce the production of phages and phage-encoded products, disseminating these viruses and virulence-related genes, which have dangerous consequences for disease severity. These unwanted side-effects of antibiotics cast doubt on the suitability of some antimicrobial treatments and may require new strategies to prevent and limit the selection for virulence. Foremost among these treatments is phage therapy, which could be used to treat many bacterial infectious diseases and confront the pressing problem of antibiotic resistance in pathogenic bacteria. This review discusses the interactions between bacteriophages, antibiotics, and bacteria and provides an integrated perspective that aims to inspire the development of successful antibacterial therapies.
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41
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Wei Z, Feng K, Li S, Zhang Y, Chen H, Yin H, Xu M, Deng Y. Exploring abundance, diversity and variation of a widespread antibiotic resistance gene in wastewater treatment plants. ENVIRONMENT INTERNATIONAL 2018; 117:186-195. [PMID: 29753149 DOI: 10.1016/j.envint.2018.05.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/24/2018] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
An updated sul1 gene sequence database was constructed and new degenerate primers were designed to better investigate the abundance, diversity, and variation of a ubiquitous antibiotic resistance gene, sul1, with PCR-based methods in activated sludge from wastewater treatment plants (WWTPs). The newly designed degenerate primers showed high specificity and higher coverage in both in-silico evaluations and activated sludge samples compared to previous sul1 primers. Using the new primers, the abundance and diversity of sul1 gene, together with 16S rRNA gene, in activated sludge from five WWTPs in summer and winter were determined by quantitative PCR and MiSeq sequencing. The sul1 gene was found to be prevalent and displayed a comparable abundance (0.081 copies per bacterial cell in average) to the total bacteria across all samples. However, compared to the significant seasonal and geographical divergences in the quantity and diversity of bacterial communities in WWTPs, there were no significant seasonal or geographical variations of representative clusters of sul1 gene in most cases. Additionally, the representative sul1 clusters showed fairly close phylogeny and there was no obvious correlation between sul1 gene and the dominant bacterial genera, as well as the int1 gene, suggesting that bacterial hosts of sul1 gene is not stable, the sul1 gene may be carried by mobile genetic elements, sometimes integrated with class 1 integrons and sometimes not. Thus mobile genetic elements likely play a greater role than specific microbial taxa in determining the composition of sul1 gene in WWTPs.
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Affiliation(s)
- Ziyan Wei
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Feng
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuzhen Li
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongrui Chen
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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Yang Y, Song W, Lin H, Wang W, Du L, Xing W. Antibiotics and antibiotic resistance genes in global lakes: A review and meta-analysis. ENVIRONMENT INTERNATIONAL 2018; 116:60-73. [PMID: 29653401 DOI: 10.1016/j.envint.2018.04.011] [Citation(s) in RCA: 362] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 04/06/2018] [Accepted: 04/06/2018] [Indexed: 05/17/2023]
Abstract
Lakes are an important source of freshwater, containing nearly 90% of the liquid surface fresh water worldwide. Long retention times in lakes mean pollutants from discharges slowly circulate around the lakes and may lead to high ecological risk for ecosystem and human health. In recent decades, antibiotics and antibiotic resistance genes (ARGs) have been regarded as emerging pollutants. The occurrence and distribution of antibiotics and ARGs in global freshwater lakes are summarized to show the pollution level of antibiotics and ARGs and to identify some of the potential risks to ecosystem and human health. Fifty-seven antibiotics were reported at least once in the studied lakes. Our meta-analysis shows that sulfamethoxazole, sulfamerazine, sulfameter, tetracycline, oxytetracycline, erythromycin, and roxithromycin were found at high concentrations in both lake water and lake sediment. There is no significant difference in the concentration of sulfonamides in lake water from China and that from other countries worldwide; however, there was a significant difference in quinolones. Erythromycin had the lowest predicted hazardous concentration for 5% of the species (HC5) and the highest ecological risk in lakes. There was no significant difference in the concentration of sulfonamide resistance genes (sul1 and sul2) in lake water and river water. There is surprisingly limited research on the role of aquatic biota in propagation of ARGs in freshwater lakes. As an environment that is susceptible to cumulative build-up of pollutants, lakes provide an important environment to study the fate of antibiotics and transport of ARGs with a broad range of niches including bacterial community, aquatic plants and animals.
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Affiliation(s)
- Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.
| | - Wenjuan Song
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Hui Lin
- Institute of Environmental Resources and Soil Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Weibo Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Linna Du
- Department of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology, Wenzhou 325006, China
| | - Wei Xing
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
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Wang M, Liu P, Zhou Q, Tao W, Sun Y, Zeng Z. Estimating the contribution of bacteriophage to the dissemination of antibiotic resistance genes in pig feces. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 238:291-298. [PMID: 29573711 DOI: 10.1016/j.envpol.2018.03.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 03/07/2018] [Accepted: 03/08/2018] [Indexed: 05/04/2023]
Abstract
The transfer of antibiotic resistance genes (ARGs) in the environment is a threat to both human and animal health. However, the contribution of bacteriophages to the dissemination of resistance genes via transduction is rarely explored. In this study, we screened pig feces from three commercial farms in China for 32 clinically relevant ARG types to assess the presence of the ARG population in bacteria and bacteriophage and further to estimate the contribution of bacteriophages to the dissemination of antibiotic resistance. We found that bacteriophage DNA contained 35.5% of the target ARG types and sul1, blaTEM and ermB were found in 100% of the phage DNA samples. The most abundant genes in the bacterial population were ermB and fexA whereas ermB was the most abundant in bacteriophage. In contrast, floR was the least abundant ARG in both populations. Also, the ratio index of the abundance of ARGs in bacteriophage and bacteria was firstly used in this study as an estimator of bacteriophage ability to transmit ARGs. The ratio for qnrA was the greatest (about 10-1) and differed from the most abundant bacteriophage ARG ermB. In addition, fexA had the lowest ratio value (about 10-6) and not floR. These results illustrate that ARGs abundance and detection rates used alone probably be not suitable for comprehensively judging the contribution of bacteriophage to the dissemination of antibiotic resistance. A more suitable model is the application of three indices; occurrence rate, absolute abundance in bacteriophage and the ratio value as warning and monitoring tools for environmental ARG assessments in bacteriophages.
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Affiliation(s)
- Mianzhi Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Peng Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Qin Zhou
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Wanyu Tao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Yongxue Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China.
| | - Zhenling Zeng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China.
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Wu D, Ma R, Wei H, Yang K, Xie B. Simulated discharge of treated landfill leachates reveals a fueled development of antibiotic resistance in receiving tidal river. ENVIRONMENT INTERNATIONAL 2018; 114:143-151. [PMID: 29501852 DOI: 10.1016/j.envint.2018.02.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/02/2018] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Abstract
Around 350 million tons of solid waste is disposed of in landfills every year globally, with millions of cubic meters of landfill leachates released into neighboring environment. However, to date, little is known about the variations of antimicrobial resistance (AMR) in on-site leachate treatment systems and its development in leachate-receiving water environment. Here, we quantified 7 subtypes of antibiotic resistance genes (ARGs), 3 types of culturable antibiotic resistant bacteria (ARB) and 6 subtypes of mobile genetic elements (MGEs) in the effluents from a combined leachate treatment process, including biological treatment (MBR), physical separation (UF), ultraviolet (UV) disinfection and advanced oxidation process (AOP). The contents of ARGs, ARB and MGEs were generally enriched by the MBR, but then decreased significantly along with the tertiary treatment process. However, in the effluent-receiving water samples, the abundance of dominant ARGs (i.e. ermB, sul1, blaTEM) increased by 1.5 orders of magnitude within 96 h, alongside a general increase of MGEs (~10.0 log10(copies/mL) and total ARB (~1100 CFU/mL). Structural correlation analyses reveal that target ARGs were closely associated with MGEs, particularly in effluent-receiving samples (Procrustes test; M2 = 0.49, R = 0.71, P = 0.001); and occurrences of ARB were majorly affected by ARG's distribution and environmental conditions (e.g. nitrogen speciation) in effluent and recipient groups, respectively. This study indicates that current treatment technologies and operation protocols are not feasible in countering the development of AMR in effluent-receiving water environment, particularly in tidal rivers that are capable of retaining contaminants for a long residence time.
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Affiliation(s)
- Dong Wu
- Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; Joint Research Institute for New Energy and the Environment, East China Normal University and Colorado State University, Shanghai 200062, China
| | - Ruoqi Ma
- Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, China
| | - Huawei Wei
- Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Kai Yang
- Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; Joint Research Institute for New Energy and the Environment, East China Normal University and Colorado State University, Shanghai 200062, China
| | - Bing Xie
- Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; Joint Research Institute for New Energy and the Environment, East China Normal University and Colorado State University, Shanghai 200062, China.
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Brown-Jaque M, Rodriguez Oyarzun L, Cornejo-Sánchez T, Martín-Gómez MT, Gartner S, de Gracia J, Rovira S, Alvarez A, Jofre J, González-López JJ, Muniesa M. Detection of Bacteriophage Particles Containing Antibiotic Resistance Genes in the Sputum of Cystic Fibrosis Patients. Front Microbiol 2018; 9:856. [PMID: 29765367 PMCID: PMC5938348 DOI: 10.3389/fmicb.2018.00856] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/13/2018] [Indexed: 11/13/2022] Open
Abstract
Cystic fibrosis (CF) is a chronic disease in which the bacterial colonization of the lung is linked to an excessive inflammatory response that leads to respiratory failure. The microbiology of CF is complex. Staphylococcus aureus is the first bacterium to colonize the lungs in 30% of pediatric CF patients, and 80% of adult patients develop a chronic Pseudomonas aeruginosa infection, but other microorganisms can also be found. The use of antibiotics is essential to treat the disease, but antibiotic performance is compromised by resistance mechanisms. Among various mechanisms of transfer of antibiotic resistance genes (ARGs), the recently been reported bacteriophages are the least explored in clinical settings. To determine the role of phages in CF as mobile genetic elements (MGEs) carrying ARGs, we evaluated their presence in 71 CF patients. 71 sputum samples taken from these patients were screened for eight ARGs (blaTEM, blaCTX-M-1-group, blaCTX-M-9-group, blaOXA-48, blaVIM, mecA, qnrA, and qnrS) in the bacteriophage DNA fraction. The phages found were also purified and observed by electron microscopy. 32.4% of CF patients harbored ARGs in phage DNA. β-lactamase genes, particularly blaVIM and blaTEM, were the most prevalent and abundant, whereas mecA, qnrA, and qnrS were very rare. Siphoviridae phage particles capable of infecting P. aeruginosa and Klebsiella pneumoniae were detected in CF sputum. Phage particles harboring ARGs were found to be abundant in the lungs of both CF patients and healthy individuals and could contribute to the colonization of multiresistant strains.
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Affiliation(s)
- Maryury Brown-Jaque
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Lirain Rodriguez Oyarzun
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Thais Cornejo-Sánchez
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria T Martín-Gómez
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Silvia Gartner
- Cystic Fibrosis Unit, Hospital Universitario Vall d'Hebron, Universitat Autònoma de Barcelona, CIBER of Respiratory Diseases (Ciberes CB06/06/0030), Carlos III Health Institute, Barcelona, Spain
| | - Javier de Gracia
- Cystic Fibrosis Unit, Hospital Universitario Vall d'Hebron, Universitat Autònoma de Barcelona, CIBER of Respiratory Diseases (Ciberes CB06/06/0030), Carlos III Health Institute, Barcelona, Spain
| | - Sandra Rovira
- Cystic Fibrosis Unit, Hospital Universitario Vall d'Hebron, Universitat Autònoma de Barcelona, CIBER of Respiratory Diseases (Ciberes CB06/06/0030), Carlos III Health Institute, Barcelona, Spain
| | - Antonio Alvarez
- Cystic Fibrosis Unit, Hospital Universitario Vall d'Hebron, Universitat Autònoma de Barcelona, CIBER of Respiratory Diseases (Ciberes CB06/06/0030), Carlos III Health Institute, Barcelona, Spain
| | - Joan Jofre
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Juan J González-López
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
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Zhou W, Liu L, Feng Y, Zong Z. A P7 Phage-Like Plasmid Carrying mcr-1 in an ST15 Klebsiella pneumoniae Clinical Isolate. Front Microbiol 2018; 9:11. [PMID: 29403463 PMCID: PMC5786510 DOI: 10.3389/fmicb.2018.00011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 01/05/2018] [Indexed: 02/05/2023] Open
Abstract
A Klebsiella pneumoniae clinical strain, named SCKP83, was isolated and found to be resistant to colistin thanks to the presence plasmid-borne colistin resistant gene mcr-1. The strain was subjected to whole genome sequencing and conjugation experiments. The subsequent analysis indicated that the strain belongs to ST15 and the capsular type K41. In SCKP83, mcr-1 was carried by a 97.4-kb non-self-transmissible plasmid, a 90.9-kb region of which was predicted as an intact phage. This phage was 47.79% GC content, encoded 105 proteins and contained three tRNAs. mcr-1 was located downstream of two copies of the insertion sequence ISApl1 (one complete and one truncated) and was inserted in the ant1 gene, which encodes a putative antirepressor for antagonizing C1 repression, in this phage. The phage is highly similar to phage P7 (77% coverage and 98% identity) from Escherichia coli. Several similar mcr-1-carrying plasmids have been found in E. coli at various locations in China, suggesting that these phage-like plasmids have circulated in China. The findings in this study suggest that the P7 phage-like plasmids are not restricted to E. coli and may represent new vehicles to mediate the inter-species spread of mcr-1.
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Affiliation(s)
- Weilong Zhou
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Lu Liu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Yu Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.,Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China.,Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
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47
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Peterson E, Kaur P. Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens. Front Microbiol 2018; 9:2928. [PMID: 30555448 DOI: 10.3389/fmicb.2018.02928/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 05/20/2023] Open
Abstract
Emergence of antibiotic resistant pathogenic bacteria poses a serious public health challenge worldwide. However, antibiotic resistance genes are not confined to the clinic; instead they are widely prevalent in different bacterial populations in the environment. Therefore, to understand development of antibiotic resistance in pathogens, we need to consider important reservoirs of resistance genes, which may include determinants that confer self-resistance in antibiotic producing soil bacteria and genes encoding intrinsic resistance mechanisms present in all or most non-producer environmental bacteria. While the presence of resistance determinants in soil and environmental bacteria does not pose a threat to human health, their mobilization to new hosts and their expression under different contexts, for example their transfer to plasmids and integrons in pathogenic bacteria, can translate into a problem of huge proportions, as discussed in this review. Selective pressure brought about by human activities further results in enrichment of such determinants in bacterial populations. Thus, there is an urgent need to understand distribution of resistance determinants in bacterial populations, elucidate resistance mechanisms, and determine environmental factors that promote their dissemination. This comprehensive review describes the major known self-resistance mechanisms found in producer soil bacteria of the genus Streptomyces and explores the relationships between resistance determinants found in producer soil bacteria, non-producer environmental bacteria, and clinical isolates. Specific examples highlighting potential pathways by which pathogenic clinical isolates might acquire these resistance determinants from soil and environmental bacteria are also discussed. Overall, this article provides a conceptual framework for understanding the complexity of the problem of emergence of antibiotic resistance in the clinic. Availability of such knowledge will allow researchers to build models for dissemination of resistance genes and for developing interventions to prevent recruitment of additional or novel genes into pathogens.
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Affiliation(s)
- Elizabeth Peterson
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, United States
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Auguet O, Pijuan M, Borrego CM, Rodriguez-Mozaz S, Triadó-Margarit X, Giustina SVD, Gutierrez O. Sewers as potential reservoirs of antibiotic resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 605-606:1047-1054. [PMID: 28709370 DOI: 10.1016/j.scitotenv.2017.06.153] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 06/19/2017] [Accepted: 06/19/2017] [Indexed: 05/06/2023]
Abstract
Wastewater transport along sewers favors the colonization of inner pipe surfaces by wastewater-derived microorganisms that grow forming biofilms. These biofilms are composed of rich and diverse microbial communities that are continuously exposed to antibiotic residues and antibiotic resistant bacteria (ARB) from urban wastewater. Sewer biofilms thus appear as an optimal habitat for the dispersal and accumulation of antibiotic resistance genes (ARGs). In this study, the concentration of antibiotics, integron (intI1) and antibiotic resistance genes (qnrS, sul1, sul2, blaTEM, blaKPC, ermB, tetM and tetW), and potential bacterial pathogens were analyzed in wastewater and biofilm samples collected at the inlet and outlet sections of a pressurized sewer pipe. The most abundant ARGs detected in both wastewater and biofilm samples were sul1 and sul2 with roughly 1 resistance gene for each 10 copies of 16s RNA gene. Significant differences in the relative abundance of gene intI1 and genes conferring resistance to fluoroquinolones (qnrS), sulfonamides (sul1 and sul2) and betalactams (blaTEM) were only measured between inlet and outlet biofilm samples. Composition of bacterial communities also showed spatial differences in biofilms and a higher prevalence of Operational Taxonomic Units (OTUs) with high sequence identity (>98%) to well-known human pathogens was observed in biofilms collected at the inlet pipe section. Our study highlights the role of sewer biofilms as source and sink of ARB and ARGs and supports the idea that community composition rather than antibiotic concentration is the main factor driving the diversity of the sewage resistome.
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Affiliation(s)
- Olga Auguet
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
| | - Maite Pijuan
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Sara Rodriguez-Mozaz
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
| | - Xavier Triadó-Margarit
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain; Integrative Freshwater Ecology Group, Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain
| | - Saulo Varela Della Giustina
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
| | - Oriol Gutierrez
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain.
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Rodríguez-Rubio L, Jofre J, Muniesa M. Is Genetic Mobilization Considered When Using Bacteriophages in Antimicrobial Therapy? Antibiotics (Basel) 2017; 6:antibiotics6040032. [PMID: 29206153 PMCID: PMC5745475 DOI: 10.3390/antibiotics6040032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/15/2017] [Accepted: 12/04/2017] [Indexed: 01/19/2023] Open
Abstract
The emergence of multi-drug resistant bacteria has undermined our capacity to control bacterial infectious diseases. Measures needed to tackle this problem include controlling the spread of antibiotic resistance, designing new antibiotics, and encouraging the use of alternative therapies. Phage therapy seems to be a feasible alternative to antibiotics, although there are still some concerns and legal issues to overcome before it can be implemented on a large scale. Here we highlight some of those concerns, especially those related to the ability of bacteriophages to transport bacterial DNA and, in particular, antibiotic resistance genes.
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Affiliation(s)
- Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Joan Jofre
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Av. Diagonal 643, 08028 Barcelona, Spain.
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50
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Wu D, Dolfing J, Xie B. Bacterial perspectives on the dissemination of antibiotic resistance genes in domestic wastewater bio-treatment systems: beneficiary to victim. Appl Microbiol Biotechnol 2017; 102:597-604. [DOI: 10.1007/s00253-017-8665-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 11/24/2022]
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