1
|
Ransirini AM, Elżbieta MS, Joanna G, Bartosz K, Wojciech T, Agnieszka B, Magdalena U. Fertilizing drug resistance: Dissemination of antibiotic resistance genes in soil and plant bacteria under bovine and swine slurry fertilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174476. [PMID: 38969119 DOI: 10.1016/j.scitotenv.2024.174476] [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: 03/12/2024] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
The increasing global demand for food production emphasizes the use of organic animal fertilizers, such as manure and slurry, to support sustainable agricultural practices. However, recent studies highlight concerns about antibiotic resistance determinants in animal excrements, posing a potential risk of spreading antibiotic resistance genes (ARGs) in agricultural soil and, consequently, in food products. This study examines the dissemination of ARGs within the soil and plant-associated microbiomes in cherry radish following the application of swine and bovine slurry. In a 45-day pot experiment, slurry-amended soil, rhizospheric bacteria, and endophytic bacteria in radish roots and leaves were sampled and analyzed for 21 ARGs belonging to 7 Antibiotic Resistance Phenotypes (ARPs). The study also assessed slurry's impact on soil microbiome functional diversity, enzymatic activity, physicochemical soil parameters, and the concentration of 22 selected antimicrobials in soil and plant tissues. Tetracyclines and β-lactams were the most frequently identified ARGs in bovine and swine slurry, aligning with similar studies worldwide. Swine slurry showed a higher prevalence of ARGs in soil and plant-associated bacteria, particularly TET genes, reflecting pig antibiotic treatments. The persistent dominance of TET genes across slurry, soil, and plant microbiomes highlights significant influence of slurry application on gene occurrence in plant bacteria. The presence of ARGs in edible plant parts underscores health risks associated with raw vegetable consumption. Time-dependent dynamics of ARG occurrence highlighted their persistent presence throughout the experiment duration, influenced by the environmental factors and antibiotic residuals. Notably, ciprofloxacin, which was the only one antimicrobial detected in fertilized soil, significantly impacted bovine-amended variants. Soil salinity modifications induced by slurry application correlated with changes in ARG occurrence. Overall, the research underscores the complex relationships between agricultural practices, microbial activity, and antibiotic resistance dissemination, emphasizing the need for a more sustainable and health-conscious farming approaches.
Collapse
Affiliation(s)
- Attanayake Mudiyanselage Ransirini
- University of Lodz, Faculty of Biology and Environmental Protection, UNESCO Chair on Ecohydrology and Applied Ecology, Banacha 12/16, 90-237 Lodz, Poland
| | - Mierzejewska-Sinner Elżbieta
- University of Lodz, Faculty of Biology and Environmental Protection, UNESCO Chair on Ecohydrology and Applied Ecology, Banacha 12/16, 90-237 Lodz, Poland
| | - Giebułtowicz Joanna
- Medical University of Warsaw, Faculty of Pharmacy, Department of Drug Chemistry, Pharmaceutical and Biomedical Analysis, Banacha 1, 02-097 Warsaw, Poland
| | - Kózka Bartosz
- Medical University of Warsaw, Faculty of Pharmacy, Department of Drug Chemistry, Pharmaceutical and Biomedical Analysis, Banacha 1, 02-097 Warsaw, Poland
| | - Tołoczko Wojciech
- Department of Physical Geography, Faculty of Geography, University of Lodz, Prez. Gabriela Narutowicza 88, 90-139, Lodz, Poland
| | - Bednarek Agnieszka
- University of Lodz, Faculty of Biology and Environmental Protection, UNESCO Chair on Ecohydrology and Applied Ecology, Banacha 12/16, 90-237 Lodz, Poland
| | - Urbaniak Magdalena
- University of Lodz, Faculty of Biology and Environmental Protection, UNESCO Chair on Ecohydrology and Applied Ecology, Banacha 12/16, 90-237 Lodz, Poland.
| |
Collapse
|
2
|
Naidoo Y, Pierneef RE, Cowan DA, Valverde A. Characterization of the soil resistome and mobilome in Namib Desert soils. Int Microbiol 2024; 27:967-975. [PMID: 37968548 PMCID: PMC11300574 DOI: 10.1007/s10123-023-00454-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023]
Abstract
The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.
Collapse
Affiliation(s)
- Yashini Naidoo
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
| | - Rian E Pierneef
- Biotechnology Platform, Agricultural Research Council, Soutpan Road, Onderstepoort Campus, Pretoria, 0110, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Angel Valverde
- IRNASA-CSIC, Cordel de Merinas, 37008, Salamanca, Spain.
| |
Collapse
|
3
|
Musiyiwa K, Simbanegavi TT, Marumure J, Makuvara Z, Chaukura N, Gwenzi W. The soil-microbe-plant resistome: A focus on the source-pathway-receptor continuum. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:12666-12682. [PMID: 38253827 DOI: 10.1007/s11356-023-31788-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024]
Abstract
The One World, One Health concept implies that antibiotic resistance (AR) in the soil-microbe-plant resistome is intricately linked to the human resistome. However, the literature is mainly confined to sources and types of AR in soils or microbes, but comprehensive reviews tracking AR in the soil-microbe-plant resistome are limited. The present review applies the source-pathway-receptor concept to understand the sources, behaviour, and health hazards of the soil-microbe-plant resistome. The results showed that the soil-microbe-plant system harbours various antibiotic-resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and mobile genetic elements (MGEs). Anthropogenic sources and drivers include soil application of solid waste, wastewater, biosolids, and industrial waste. Water-, wind-, and human-driven processes and horizontal gene transfer circulate AR in the soil-microbe-plant resistome. The AR in bulk soil, soil components that include soil microorganisms, soil meso- and macro-organisms, and possible mechanisms of AR transfer to soil components and ultimately to plants are discussed. The health risks of the soil-microbe-plant resistome are less studied, but potential impacts include (1) the transfer of AR to previously susceptible organisms and other resistomes, including the human resistome. Overall, the study tracks the behaviour and health risks of AR in the soil-plant system. Future research should focus on (1) ecological risks of AR at different levels of biological organization, (2) partitioning of AR among various phases of the soil-plant system, (3) physico-chemical parameters controlling the fate of AR, and (4) increasing research from low-income regions particularly Africa as most of the available literature is from developed countries.
Collapse
Affiliation(s)
- Kumbirai Musiyiwa
- Department of Crop Science and Post-Harvest Technology, School of Agricultural Science and Technology, Chinhoyi University of Technology, Private Bag 7724, Chinhoyi, Zimbabwe
| | - Tinoziva T Simbanegavi
- Department of Soil Science and Environment, Faculty of Agriculture, Environment, and Food Systems, University of Zimbabwe, Mt. Pleasant, P.O. Box MP167, Harare, Zimbabwe
| | - Jerikias Marumure
- Department of Physics, Geography and Environmental Science, School of Natural Sciences, Great Zimbabwe University, P.O. Box 1235, Masvingo, Zimbabwe
- Department of Life and Consumer Sciences, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Pretoria, South Africa
| | - Zakio Makuvara
- Department of Physics, Geography and Environmental Science, School of Natural Sciences, Great Zimbabwe University, P.O. Box 1235, Masvingo, Zimbabwe
- Department of Life and Consumer Sciences, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Pretoria, South Africa
| | - Nhamo Chaukura
- Department of Physical and Earth Sciences, Sol Plaatje University, Kimberley, 8301, South Africa
| | - Willis Gwenzi
- Grassland Science and Renewable Plant Resources, Universitat Kassel, Steinstraβe 19, 37213, Witzenhausen, Germany.
| |
Collapse
|
4
|
Castañeda-Molina Y, Marulanda-Moreno SM, Saldamando-Benjumea C, Junca H, Moreno-Herrera CX, Cadavid-Restrepo G. Microbiome analysis of Spodoptera frugiperda (Lepidoptera, Noctuidae) larvae exposed to Bacillus thuringiensis (Bt) endotoxins. PeerJ 2023; 11:e15916. [PMID: 37719127 PMCID: PMC10503500 DOI: 10.7717/peerj.15916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/27/2023] [Indexed: 09/19/2023] Open
Abstract
Background Spodoptera frugiperda (or fall armyworm, FAW) is a polyphagous pest native to Western Hemisphere and recently discovered in the Eastern Hemisphere. In Colombia, S. frugiperda is recognized as a pest of economic importance in corn. The species has genetically differentiated into two host populations named "corn" and "rice" strains. In 2012, a study made in central Colombia demonstrated that the corn strain is less susceptible to Bacillus thuringiensis (Bt) endotoxins (Cry1Ac and Cry 1Ab) than the rice strain. In this country, Bt transgenic corn has been extensively produced over the last 15 years. Since gut microbiota plays a role in the physiology and immunity of insects, and has been implicated in promoting the insecticidal activity of Bt, in this study an analysis of the interaction between Bt endotoxins and FAW gut microbiota was made. Also, the detection of endosymbionts was performed here, as they might have important implications in the biological control of a pest. Methods The composition and diversity of microbiomes associated with larval specimens of S. frugiperda(corn strain) was investigated in a bioassay based on six treatments in the presence/absence of Bt toxins and antibiotics (Ab) through bacterial isolate analyses and by high throughput sequencing of the bacterial 16S rRNA gene. Additionally, species specific primers were used, to detect endosymbionts from gonads in S. frugiperda corn strain. Results Firmicutes, Proteobacteria and Bacteroidota were the most dominant bacterial phyla found in S. frugiperda corn strain. No significant differences in bacteria species diversity and richness among the six treatments were found. Two species of Enterococcus spp., E. mundtii and E. casseliflavus were detected in treatments with Bt and antibiotics, suggesting that they are less susceptible to both of them. Additionally, the endosymbiont Arsenophonus was also identified on treatments in presence of Bt and antibiotics. The results obtained here are important since little knowledge exists about the gut microbiota on this pest and its interaction with Bt endotoxins. Previous studies made in Lepidoptera suggest that alteration of gut microbiota can be used to improve the management of pest populations, demonstrating the relevance of the results obtained in this work.
Collapse
Affiliation(s)
- Yuliana Castañeda-Molina
- Departamento de Biociencias/Grupo de investigación Microbiodiversidad y Bioprospección/Laboratorio de Biología Celular y Molecular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| | - Sandra María Marulanda-Moreno
- Departamento de Biociencias/Grupo de investigación Microbiodiversidad y Bioprospección/Laboratorio de Biología Celular y Molecular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| | - Clara Saldamando-Benjumea
- Departamento de Biociencias/Grupo de Biotecnologia Vegetal UNALMED-CIB/Laboratorio de Ecología y Evolución de Insectos, Universidad Nacional de Colombia, Medellin, Antioquia, Colombia
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div. Ecogenomics & Holobionts, Microbiomas Foundation, Chía, Cundinamarca, Colombia
| | - Claudia Ximena Moreno-Herrera
- Departamento de Biociencias/Grupo de investigación Microbiodiversidad y Bioprospección/Laboratorio de Biología Celular y Molecular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| | - Gloria Cadavid-Restrepo
- Departamento de Biociencias/Grupo de investigación Microbiodiversidad y Bioprospección/Laboratorio de Biología Celular y Molecular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| |
Collapse
|
5
|
Sindhu SS, Sehrawat A, Glick BR. The involvement of organic acids in soil fertility, plant health and environment sustainability. Arch Microbiol 2022; 204:720. [DOI: 10.1007/s00203-022-03321-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/22/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022]
|
6
|
Transgenic Improvement for Biotic Resistance of Crops. Int J Mol Sci 2022; 23:ijms232214370. [PMID: 36430848 PMCID: PMC9697442 DOI: 10.3390/ijms232214370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Biotic constraints, including pathogenic fungi, viruses and bacteria, herbivory insects, as well as parasitic nematodes, cause significant yield loss and quality deterioration of crops. The effect of conventional management of these biotic constraints is limited. The advances in transgenic technologies provide a direct and directional approach to improve crops for biotic resistance. More than a hundred transgenic events and hundreds of cultivars resistant to herbivory insects, pathogenic viruses, and fungi have been developed by the heterologous expression of exogenous genes and RNAi, authorized for cultivation and market, and resulted in a significant reduction in yield loss and quality deterioration. However, the exploration of transgenic improvement for resistance to bacteria and nematodes by overexpression of endogenous genes and RNAi remains at the testing stage. Recent advances in RNAi and CRISPR/Cas technologies open up possibilities to improve the resistance of crops to pathogenic bacteria and plant parasitic nematodes, as well as other biotic constraints.
Collapse
|
7
|
Brugiroux S, Berry D, Ring D, Barnich N, Daims H, Stecher B. Specific Localization and Quantification of the Oligo-Mouse-Microbiota (OMM 12 ) by Fluorescence In Situ Hybridization (FISH). Curr Protoc 2022; 2:e548. [PMID: 36094300 DOI: 10.1002/cpz1.548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The oligo-mouse-microbiota (OMM12 ) is a widely used syncom that colonizes gnotobiotic mice in a stable manner. It provides several fundamental functions to its murine host, including colonization resistance against enteric pathogens. Here, we designed and validated specific fluorescence in situ hybridization (FISH) probes to detect and quantify OMM12 strains on intestinal tissue cross sections. 16S rRNA-specific probes were designed, and specificity was validated on fixed pure cultures. A hybridization protocol was optimized for sensitive detection of the individual bacterial cells in cryosections. Using this method, we showed that the intestinal mucosal niche of Akkermansia muciniphila can be influenced by global gut microbial community context. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Localization and quantification of OMM12 single strains in mouse cecum cross section Support Protocol: Establishment of specific FISH probe set for OMM12 syncom.
Collapse
Affiliation(s)
- Sandrine Brugiroux
- Max von Pettenkofer Institute, LMU Munich, Munich, Germany
- M2iSH, UMR 1071 Inserm, University of Clermont Auvergne, Clermont-Ferrand, France
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Diana Ring
- Max von Pettenkofer Institute, LMU Munich, Munich, Germany
| | - Nicolas Barnich
- M2iSH, UMR 1071 Inserm, University of Clermont Auvergne, Clermont-Ferrand, France
| | - Holger Daims
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Bärbel Stecher
- Max von Pettenkofer Institute, LMU Munich, Munich, Germany
- German Center for Infection Research, Partner Site Munich, Germany
| |
Collapse
|
8
|
Philips JG, Martin-Avila E, Robold AV. Horizontal gene transfer from genetically modified plants - Regulatory considerations. Front Bioeng Biotechnol 2022; 10:971402. [PMID: 36118580 PMCID: PMC9471246 DOI: 10.3389/fbioe.2022.971402] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Gene technology regulators receive applications seeking permission for the environmental release of genetically modified (GM) plants, many of which possess beneficial traits such as improved production, enhanced nutrition and resistance to drought, pests and diseases. The regulators must assess the risks to human and animal health and to the environment from releasing these GM plants. One such consideration, of many, is the likelihood and potential consequence of the introduced or modified DNA being transferred to other organisms, including people. While such gene transfer is most likely to occur to sexually compatible relatives (vertical gene transfer), horizontal gene transfer (HGT), which is the acquisition of genetic material that has not been inherited from a parent, is also a possibility considered during these assessments. Advances in HGT detection, aided by next generation sequencing, have demonstrated that HGT occurrence may have been previously underestimated. In this review, we provide updated evidence on the likelihood, factors and the barriers for the introduced or modified DNA in GM plants to be horizontally transferred into a variety of recipients. We present the legislation and frameworks the Australian Gene Technology Regulator adheres to with respect to the consideration of risks posed by HGT. Such a perspective may generally be applicable to regulators in other jurisdictions as well as to commercial and research organisations who develop GM plants.
Collapse
|
9
|
Yu H, Yang Q, Fu F, Li W. Three strategies of transgenic manipulation for crop improvement. FRONTIERS IN PLANT SCIENCE 2022; 13:948518. [PMID: 35937379 PMCID: PMC9354092 DOI: 10.3389/fpls.2022.948518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Heterologous expression of exogenous genes, overexpression of endogenous genes, and suppressed expression of undesirable genes are the three strategies of transgenic manipulation for crop improvement. Up to 2020, most (227) of the singular transgenic events (265) of crops approved for commercial release worldwide have been developed by the first strategy. Thirty-eight of them have been transformed by synthetic sequences transcribing antisense or double-stranded RNAs and three by mutated copies for suppressed expression of undesirable genes (the third strategy). By the first and the third strategies, hundreds of transgenic events and thousands of varieties with significant improvement of resistance to herbicides and pesticides, as well as nutritional quality, have been developed and approved for commercial release. Their application has significantly decreased the use of synthetic pesticides and the cost of crop production and increased the yield of crops and the benefits to farmers. However, almost all the events overexpressing endogenous genes remain at the testing stage, except one for fertility restoration and another for pyramiding herbicide tolerance. The novel functions conferred by the heterologously expressing exogenous genes under the control of constitutive promoters are usually absent in the recipient crops themselves or perform in different pathways. However, the endogenous proteins encoded by the overexpressing endogenous genes are regulated in complex networks with functionally redundant and replaceable pathways and are difficult to confer the desirable phenotypes significantly. It is concluded that heterologous expression of exogenous genes and suppressed expression by RNA interference and clustered regularly interspaced short palindromic repeats-cas (CRISPR/Cas) of undesirable genes are superior to the overexpression of endogenous genes for transgenic improvement of crops.
Collapse
Affiliation(s)
| | | | - Fengling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wanchen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
10
|
Current Techniques to Study Beneficial Plant-Microbe Interactions. Microorganisms 2022; 10:microorganisms10071380. [PMID: 35889099 PMCID: PMC9317800 DOI: 10.3390/microorganisms10071380] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Many different experimental approaches have been applied to elaborate and study the beneficial interactions between soil bacteria and plants. Some of these methods focus on changes to the plant and others are directed towards assessing the physiology and biochemistry of the beneficial plant growth-promoting bacteria (PGPB). Here, we provide an overview of some of the current techniques that have been employed to study the interaction of plants with PGPB. These techniques include the study of plant microbiomes; the use of DNA genome sequencing to understand the genes encoded by PGPB; the use of transcriptomics, proteomics, and metabolomics to study PGPB and plant gene expression; genome editing of PGPB; encapsulation of PGPB inoculants prior to their use to treat plants; imaging of plants and PGPB; PGPB nitrogenase assays; and the use of specialized growth chambers for growing and monitoring bacterially treated plants.
Collapse
|
11
|
Grigorenko VG, Petrova TE, Carolan C, Rubtsova MY, Uporov IV, Pereira J, Chojnowski G, Samygina VR, Lamzin VS, Egorov AM. Crystal structures of the molecular class A β-lactamase TEM-171 and its complexes with tazobactam. Acta Crystallogr D Struct Biol 2022; 78:825-834. [DOI: 10.1107/s2059798322004879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/06/2022] [Indexed: 11/10/2022] Open
Abstract
The resistance of bacteria to β-lactam antibiotics is primarily caused by the production of β-lactamases. Here, novel crystal structures of the native β-lactamase TEM-171 and two complexes with the widely used inhibitor tazobactam are presented, alongside complementary data from UV spectroscopy and fluorescence quenching. The six chemically identical β-lactamase molecules in the crystallographic asymmetric unit displayed different degrees of disorder. The tazobactam intermediate was covalently bound to the catalytic Ser70 in the trans-enamine configuration. While the conformation of tazobactam in the first complex resembled that in published β-lactamase–tazobactam structures, in the second complex, which was obtained after longer soaking of the native crystals in the inhibitor solution, a new and previously unreported tazobactam conformation was observed. It is proposed that the two complexes correspond to different stages along the deacylation path of the acyl-enzyme intermediate. The results provide a novel structural basis for the rational design of new β-lactamase inhibitors.
Collapse
|
12
|
β-Lactam Resistance in Azospirillum baldaniorum Sp245 Is Mediated by Lytic Transglycosylase and β-Lactamase and Regulated by a Cascade of RpoE7→RpoH3 Sigma Factors. J Bacteriol 2022; 204:e0001022. [PMID: 35352964 DOI: 10.1128/jb.00010-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Bacterial resistance to β-lactam antibiotics is often mediated by β-lactamases and lytic transglycosylases. Azospirillum baldaniorum Sp245 is a plant-growth-promoting rhizobacterium that shows high levels of resistance to ampicillin. Investigating the molecular basis of ampicillin resistance and its regulation in A. baldaniorum Sp245, we found that a gene encoding lytic transglycosylase (Ltg1) is organized divergently from a gene encoding an extracytoplasmic function (ECF) σ factor (RpoE7) in its genome. Inactivation of rpoE7 in A. baldaniorum Sp245 led to increased ability to form cell-cell aggregates and produce exopolysaccharides and biofilm, suggesting that rpoE7 might contribute to antibiotic resistance. Inactivation of ltg1 in A. baldaniorum Sp245, however, adversely affected its growth, indicating a requirement of Ltg1 for optimal growth. The expression of rpoE7, as well that of as ltg1, was positively regulated by RpoE7, and overexpression of RpoE7 conferred ampicillin sensitivity to both the rpoE7::km mutant and its parent. In addition, RpoE7 negatively regulated the expression of a gene encoding a β-lactamase (bla1). Out of the 5 paralogs of RpoH encoded in the genome of A. baldaniorum Sp245, RpoH3 played major roles in conferring ampicillin sensitivity and in the downregulation of bla1. The expression of rpoH3 was positively regulated by RpoE7. Collectively, these observations reveal a novel regulatory cascade of RpoE7-RpoH3 σ factors that negatively regulates ampicillin resistance in A. baldaniorum Sp245 by controlling the expression of a β-lactamase and a lytic transglycosylase. In the absence of a cognate anti-sigma factor, addressing how the activity of RpoE7 is regulated by β-lactams will unravel new mechanisms of regulation of β-lactam resistance in bacteria. IMPORTANCE Antimicrobial resistance is a global health problem that requires a better understanding of the mechanisms that bacteria use to resist antibiotics. Bacteria inhabiting the plant rhizosphere are a potential source of antibiotic resistance, but their mechanisms controlling antibiotic resistance are poorly understood. A. baldaniorum Sp245 is a rhizobacterium that is known for its characteristic resistance to ampicillin. Here, we show that an AmpC-type β-lactamase and a lytic transglycosylase mediate resistance to ampicillin in A. baldaniorum Sp245. While the gene encoding lytic transglycosylase is positively regulated by an ECF σ-factor (RpoE7), a cascade of RpoE7 and RpoH3 σ factors negatively regulates the expression of β-lactamase. This is the first evidence showing involvement of a regulatory cascade of σ factors in the regulation of ampicillin resistance in a rhizobacterium.
Collapse
|
13
|
Brady C, Orsi M, Doonan JM, Denman S, Arnold D. Brenneria goodwinii growth in vitro is improved by competitive interactions with other bacterial species associated with Acute Oak Decline. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100102. [PMID: 35005660 PMCID: PMC8717232 DOI: 10.1016/j.crmicr.2021.100102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Mutually competitive interactions prevail in pairwise cultures of AOD bacteria. In vitro growth of brenneria goodwinii is improved by bacterial competition. Co-culturing of AOD bacteria indicates evolving improved fitness of B. goodwinii. B. goodwinii and R. victoriana can collaborate in vitro to outcompete G. quercinecans.
Brenneria goodwinii, Rahnella victoriana and Gibbsiella quercinecans are three bacterial species frequently isolated together from oak displaying symptoms of Acute Oak Decline (AOD), which include weeping patches on trunks. All three bacterial species play a role in lesion formation in the current episode of AOD in Britain, although B. goodwinii is the most dominant. The ongoing research into stem lesion formation characteristic of this polybacterial syndrome has been focussed primarily on the pathogenicity, identification and taxonomy of these bacteria. As all three species were newly classified within the past ten years, there are many unanswered questions regarding their ecology and interactions with each other. To determine the effect of bacterial interactions on fitness in vitro, we examined pairwise (diculture) and multispecies (triculture) interactions between B. goodwinii, R. victoriana and G. quercinecans in oak leaf media microcosms. Additionally, the effect of co-culturing on the evolution of these species was determined and the evolved B. goodwinii strains were examined further by whole genome sequencing. Our results indicate that B. goodwinii thrived in monoculture with significantly higher viable cell counts than the other two species. Additionally, B. goodwinii performed well in pairwise culture with mutually competitive interactions observed between B. goodwinii and R. victoriana, and between B. goodwinii and G. quercinecans. In the multispecies triculture, B. goodwinii and R. victoriana appeared to exhibit co-ordinated behaviour to outcompete G. quercinecans. After four weeks B. goodwinii grown in co-culture with the other two species developed greater evolved fitness than the strain grown in monoculture as reflected by the increased viable cell counts. The competitive interactions taking place between the threes species indicated evolving improved fitness of B. goodwinii in vitro, that gave it a growth advantage over both R. victoriana and G. quercinecans which showed no significant changes in fitness. Overall, B. goodwinii gains greater benefit in terms of fitness from in vitro competitive interaction with the other two species.
Collapse
Affiliation(s)
- Carrie Brady
- Centre for Research in Bioscience, Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, United Kingdom
| | - Mario Orsi
- Centre for Research in Bioscience, Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, United Kingdom
| | - James M Doonan
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Sandra Denman
- Centre for Forestry and Climate Change, Farnham, United Kingdom
| | - Dawn Arnold
- Centre for Research in Bioscience, Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, United Kingdom.,Harper Adams University, Newport, Shropshire TF10 8NB, United Kingdom
| |
Collapse
|
14
|
Kumar S, Diksha, Sindhu SS, Kumar R. Biofertilizers: An ecofriendly technology for nutrient recycling and environmental sustainability. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 3:100094. [PMID: 35024641 PMCID: PMC8724949 DOI: 10.1016/j.crmicr.2021.100094] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 01/02/2023] Open
Abstract
Modern intensive agricultural practices face numerous challenges that pose major threats to global food security. In order to address the nutritional requirements of the ever-increasing world population, chemical fertilizers and pesticides are applied on large scale to increase crop production. However, the injudicious use of agrochemicals has resulted in environmental pollution leading to public health hazards. Moreover, agriculture soils are continuously losing their quality and physical properties as well as their chemical (imbalance of nutrients) and biological health. Plant-associated microbes with their plant growth- promoting traits have enormous potential to solve these challenges and play a crucial role in enhancing plant biomass and crop yield. The beneficial mechanisms of plant growth improvement include enhanced nutrient availability, phytohormone modulation, biocontrol of phytopathogens and amelioration of biotic and abiotic stresses. Solid-based or liquid bioinoculant formulation comprises inoculum preparation, addition of cell protectants such as glycerol, lactose, starch, a good carrier material, proper packaging and best delivery methods. Recent developments of formulation include entrapment/microencapsulation, nano-immobilization of microbial bioinoculants and biofilm-based biofertilizers. This review critically examines the current state-of-art on use of microbial strains as biofertilizers and the important roles performed by these beneficial microbes in maintaining soil fertility and enhancing crop productivity.
Collapse
Key Words
- ABA, Abscisic acid
- ACC, 1-aminocyclopropane-1-carboxylic acid
- AM, Arbuscular mycorrhiza
- APX, Ascorbate peroxidase
- BGA, Blue green algae
- BNF, Biological nitrogen fixation
- Beneficial microorganisms
- Biofertilizers
- CAT, Catalase
- Crop production
- DAPG, 2, 4-diacetyl phloroglucinol
- DRB, Deleterious rhizospheric bacteria
- GA, Gibberellic acid
- GPX, Glutathione/thioredoxin peroxidase
- HCN, Hydrogen cyanide
- IAA, Indole acetic acid
- IAR, Intrinsic antibiotic resistance
- ISR, Induced systemic resistance
- KMB, Potassium mobilizing bacteria
- KSMs, Potassium-solubilizing microbes
- MAMPs, Microbes associated molecular patterns
- PAMPs, Pathogen associated molecular patterns
- PCA, Phenazine-1-carboxylic acid
- PGP, Plant growth-promoting
- PGPR, Plant growth-promoting rhizobacteria
- POD, Peroxidase
- PSB, Phosphate-solubilizing bacteria
- Rhizosphere
- SAR, Systemic acquired resistance
- SOB, Sulphur oxidizing bacteria
- Soil fertility
- Sustainable agriculture
Collapse
Affiliation(s)
- Satish Kumar
- Department of Microbiology, CCS Haryana Agricultural University, Hisar 125004, India
| | - Diksha
- Department of Microbiology, CCS Haryana Agricultural University, Hisar 125004, India
| | - Satyavir S. Sindhu
- Department of Microbiology, CCS Haryana Agricultural University, Hisar 125004, India
| | - Rakesh Kumar
- Department of Microbiology, CCS Haryana Agricultural University, Hisar 125004, India
| |
Collapse
|
15
|
Mafiz AI, He Y, Zhang W, Zhang Y. Soil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer. Front Microbiol 2021; 12:771707. [PMID: 34887843 PMCID: PMC8650581 DOI: 10.3389/fmicb.2021.771707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/14/2021] [Indexed: 11/29/2022] Open
Abstract
Fifteen soil and 45 vegetable samples from Detroit community gardens were analyzed for potential antimicrobial resistance contamination. Soil bacteria were isolated and tested by antimicrobial susceptibility profiling, horizontal gene transfer, and whole-genome sequencing. High-throughput 16S rRNA sequencing analysis was conducted on collected soil samples to determine the total bacterial composition. Of 226 bacterial isolates recovered, 54 were from soil and 172 from vegetables. A high minimal inhibitory concentration (MIC) was defined as the MIC greater than or equal to the resistance breakpoint of Escherichia coli for Gram-negative bacteria or Staphylococcus aureus for Gram-positive bacteria. The high MIC was observed in 63.4 and 69.8% of Gram-negative isolates from soil and vegetables, respectively, against amoxicillin/clavulanic acid, as well as 97.5 and 82.7% against ampicillin, 97.6 and 90.7% against ceftriaxone, 85.4 and 81.3% against cefoxitin, 65.8 and 70.5% against chloramphenicol, and 80.5 and 59.7% against ciprofloxacin. All Gram-positive bacteria showed a high MIC to gentamicin, kanamycin, and penicillin. Forty of 57 isolates carrying tetM (70.2%) successfully transferred tetracycline resistance to a susceptible recipient via conjugation. Whole-genome sequencing analysis identified a wide array of antimicrobial resistance genes (ARGs), including those encoding AdeIJK, Mex, and SmeDEF efflux pumps, suggesting a high potential of the isolates to become antimicrobial resistant, despite some inconsistency between the gene profile and the resistance phenotype. In conclusion, soil bacteria in urban community gardens can serve as a reservoir of antimicrobial resistance with the potential to transfer to clinically important pathogens, resulting in food safety and public health concerns.
Collapse
Affiliation(s)
- Abdullah Ibn Mafiz
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, United States.,Department of Human Sciences, Tennessee State University, Nashville, TN, United States
| | - Yingshu He
- Department of Food Science and Nutrition, Illinois Institute of Technology, Chicago, IL, United States.,Center for Food Safety, University of Georgia, Griffin, GA, United States
| | - Wei Zhang
- Department of Food Science and Nutrition, Illinois Institute of Technology, Chicago, IL, United States
| | - Yifan Zhang
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, United States
| |
Collapse
|
16
|
Sapireddy V, Katuri KP, Muhammad A, Saikaly PE. Competition of two highly specialized and efficient acetoclastic electroactive bacteria for acetate in biofilm anode of microbial electrolysis cell. NPJ Biofilms Microbiomes 2021; 7:47. [PMID: 34059681 PMCID: PMC8166840 DOI: 10.1038/s41522-021-00218-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/07/2021] [Indexed: 02/04/2023] Open
Abstract
Maintaining functional stability of microbial electrolysis cell (MEC) treating wastewater depends on maintaining functional redundancy of efficient electroactive bacteria (EAB) on the anode biofilm. Therefore, investigating whether efficient EAB competing for the same resources (electron donor and acceptor) co-exist at the anode biofilm is key for the successful application of MEC for wastewater treatment. Here, we compare the electrochemical and kinetic properties of two efficient acetoclastic EAB, Geobacter sulfurreducens (GS) and Desulfuromonas acetexigens (DA), grown as monoculture in MECs fed with acetate. Additionally, we monitor the evolution of DA and GS in co-culture MECs fed with acetate or domestic wastewater using fluorescent in situ hybridization. The apparent Monod kinetic parameters reveal that DA possesses higher jmax (10.7 ± 0.4 A/m2) and lower KS, app (2 ± 0.15 mM) compared to GS biofilms (jmax: 9.6 ± 0.2 A/m2 and KS, app: 2.9 ± 0.2 mM). Further, more donor electrons are diverted to the anode for respiration in DA compared to GS. In acetate-fed co-culture MECs, DA (98% abundance) outcompete GS for anode-dependent growth. In contrast, both EAB co-exist (DA: 55 ± 2%; GS: 24 ± 1.1%) in wastewater-fed co-culture MECs despite the advantage of DA over GS based on kinetic parameters alone. The co-existence of efficient acetoclastic EAB with high current density in MECs fed with wastewater is significant in the context of functional redundancy to maintain stable performance. Our findings also provide insight to future studies on bioaugmentation of wastewater-fed MECs with efficient EAB to enhance performance.
Collapse
Affiliation(s)
- Veerraghavulu Sapireddy
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Krishna P Katuri
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
| | - Ali Muhammad
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Pascal E Saikaly
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
| |
Collapse
|
17
|
Chowdhury NN, Cox AR, Wiesner MR. Nanoparticles as vectors for antibiotic resistance: The association of silica nanoparticles with environmentally relevant extracellular antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:143261. [PMID: 33223180 DOI: 10.1016/j.scitotenv.2020.143261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/04/2020] [Accepted: 10/20/2020] [Indexed: 05/09/2023]
Abstract
A relevant but yet unconsidered subset of particles that may alter the fate of extracellular antibiotic resistance genes (eARGs) are nano-scale particles (NPs), which are ubiquitous in natural environments and have unique properties. In this study, sorption isotherms were developed describing the association of linear DNA fragments isolated from widespread eARGs (blaI and nptII) with either micon-sized kaolinite or silica nanoparticles (SNPs), to determine if sorption capacity was enhanced at the nanoscale. For each isotherm, eARG fragments were added at five starting concentrations (5-40 μg/mL) to mixed batch systems with 0.25 g of particles and nuclease-free water. Sorption was quantified by the removal of DNA from solution, as detected by a Qubit fluorimeter. Isotherms were developed for eARGs of various fragment lengths (508, 680 and 861 bp), guanine-cytosine (GC) contents (34%, 47% and 54%) and both double and single stranded eARGs, to assess the impact of DNA properties on particle association. Sorption isotherms were also developed in systems with added humic acid and/or CaCl2, to assess the impact of these environmental parameters on sorption. FTIR analysis was performed to analyze the conformation of sorbed eARGs. Desorption of eARGs was studied by quantifying the removal of eDNA from washed and vortexed post-sorption particles. Statistically significant irreversible sorption of eARGs to environmentally relevant NPs (humic acid functionalized silica nanoparticles) was demonstrated for the first time. Nano-emergent properties did not increase sorption capacity of eARGs, but led to a unique compressed conformation of sorbed eARGs. The addition of humic acid, increased CaCl2 concentration and small DNA fragment size favored sorption. NPs showed a slight preference for the sorption of single-stranded DNA over double-stranded DNA. These findings suggest that NP association with eARGs may be a significant and unique environmental phenomenon that could influence the spread of antibiotic resistance.
Collapse
Affiliation(s)
- Nadratun N Chowdhury
- Department of Civil and Environmental Engineering, Duke Hudson Hall, Box 90287, Durham, NC 27708-0287, USA.
| | - Akylah R Cox
- Department of Civil and Environmental Engineering, Duke Hudson Hall, Box 90287, Durham, NC 27708-0287, USA
| | - Mark R Wiesner
- Department of Civil and Environmental Engineering, Duke Hudson Hall, Box 90287, Durham, NC 27708-0287, USA
| |
Collapse
|
18
|
Radu E, Woegerbauer M, Rab G, Oismüller M, Strauss P, Hufnagl P, Gottsberger RA, Krampe J, Weyermair K, Kreuzinger N. Resilience of agricultural soils to antibiotic resistance genes introduced by agricultural management practices. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 756:143699. [PMID: 33307498 DOI: 10.1016/j.scitotenv.2020.143699] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/11/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
Antimicrobial resistance (AR) represents a global threat in human and veterinary medicine. In that regard, AR proliferation and dissemination in agricultural soils after manure application raises concerns on the enrichment of endogenous soil bacterial population with allochthonous antibiotic resistance genes (ARGs). Natural resilience of agricultural soils and background concentrations of ARGs play key roles in the mitigation of AR propagation in natural environments. In the present study, we carried out a longitudinal sampling campaign for two crop vegetation periods to monitor spatial and temporal changes in the abundance of seven clinically relevant ARGs (sul1, ermB, vanA, aph(3')-IIa, aph(3')-IIIa, blaTEM-1 and tet(W)) and ribosomal 16S RNA. The absolute and relative abundances of the selected ARGs were quantified in total community DNA extracted from agricultural (manured and non-manured) and forest soils, fresh pig faeces and manure slurry. We observed that ARG concentrations return to background levels after manure-induced exposure within a crop growing season, highlighting the resilience capacity of soil. Naturally occurring high background concentrations of ARGs can be found in forest soil in due distance under low anthropogenic influences. It was observed that pesticide application increases the concentrations of three out of seven ARGs tested (ermB, aph(3')-IIIa and tet(W)). Moreover, we noticed that the absolute abundances of sul1, vanA, ermB and blaTEM-1 resistance genes show an increase by 100- to 10,000- fold, from maturation of fresh pig faeces to manure. Outcomes of our study suggest that agricultural soil environments show a strong capacity to alleviate externally induced disturbances in endogenous ARG concentrations. Naturally occurring high concentrations of ARGs are present also in low human impacted environments represented by the indigenous resistome.
Collapse
Affiliation(s)
- Elena Radu
- Institute for Water Quality and Resource Management, University of Technology Vienna, Austria; Austrian Agency for Health and Food Safety AGES, Division of Data, Statistics and Risk Assessment, Department for Integrative Risk Assessment, Vienna, Austria; Institute of Virology Stefan S. Nicolau, Romanian Academy of Science, Bucharest, Romania.
| | - Markus Woegerbauer
- Austrian Agency for Health and Food Safety AGES, Division of Data, Statistics and Risk Assessment, Department for Integrative Risk Assessment, Vienna, Austria
| | - Gerhard Rab
- Institute of Hydraulic Engineering and Water Resources Management, University of Technology Vienna, Austria; Institute for Land and Water Management Research, Federal Agency for Water Management, Petzenkirchen, Austria
| | - Matthias Oismüller
- Institute of Hydraulic Engineering and Water Resources Management, University of Technology Vienna, Austria; Institute for Land and Water Management Research, Federal Agency for Water Management, Petzenkirchen, Austria
| | - Peter Strauss
- Institute for Land and Water Management Research, Federal Agency for Water Management, Petzenkirchen, Austria
| | - Peter Hufnagl
- Austrian Agency for Health and Food Safety AGES, Department for Medical Microbiology and Hygiene, Vienna, Austria
| | - Richard A Gottsberger
- Austrian Agency for Health and Food Safety AGES, Department for Molecular Diagnostic of Plant Diseases, Vienna, Austria
| | - Jörg Krampe
- Institute for Water Quality and Resource Management, University of Technology Vienna, Austria
| | - Karin Weyermair
- Austrian Agency for Health and Food Safety AGES, Division of Data, Statistics and Risk Assessment, Department of Statistics and Analytical Epidemiology, Graz, Austria
| | - Norbert Kreuzinger
- Institute for Water Quality and Resource Management, University of Technology Vienna, Austria
| |
Collapse
|
19
|
Lei Z, Karim A. The challenges and applications of nanotechnology against bacterial resistance. J Vet Pharmacol Ther 2020; 44:281-297. [PMID: 33277732 DOI: 10.1111/jvp.12936] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/30/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022]
Abstract
Bacterial resistance to the antibiotics develops rapidly and is increasingly serious health concern in the world. It is an insoluble topic due to the multiple resistant mechanisms. The overexpression of relative activities of the efflux pump has proven to be a frequent and important source of bacterial resistance. Efflux transporters in the membrane from the resistant bacteria could play a key role to inhibit the intracellular drug intake and impede the drug activities. However, nanoparticles (NPs), one of the most frequently used encapsulation materials, could increase the intracellular accumulation of the drug and inhibit the transporter activity effectively. The rational and successful application of nanotechnology is a key factor in overcoming bacterial resistance. Furthermore, nanoparticles such as metallic, carbon nanotubes and so on, may prevent the development of drug resistance and be associated with antibiotic agents, inhibiting biofilm formation or increasing the access into the target cell and exterminating the bacteria eventually. In the current study, the mechanisms of bacterial resistance are discussed and summarized. Additionally, the opportunities and challenges in the use of nanoparticles against bacterial resistance are also illuminated. At the same time, the use of nanoparticles to combat multidrug-resistant bacteria is also investigated by coupling natural antimicrobials or other alternatives. In short, we have provided a new perspective for the application of nanoparticles against multidrug-resistant bacteria.
Collapse
Affiliation(s)
- Zhiqun Lei
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Aman Karim
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| |
Collapse
|
20
|
Naidoo Y, Valverde A, Cason ED, Pierneef RE, Cowan DA. A clinically important, plasmid-borne antibiotic resistance gene (β-lactamase TEM-116) present in desert soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 719:137497. [PMID: 32114220 DOI: 10.1016/j.scitotenv.2020.137497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/20/2020] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
The exhaustive use of antibiotics in humans, animal farming and other agricultural practices has resulted in the frequent appearance of antibiotic resistant bacteria in human-impacted habitats. However, antibiotic resistance in natural (less-impacted) habitats is less understood. Using shotgun metagenomics we analysed soils from relatively low anthropogenic impact sites across the Namib Desert. We report the presence of a clinically significant extended spectrum β-lactamase (TEM-116), on a ColE1-like plasmid also carrying a metal resistance gene (arsC). The co-occurrence of resistance to antimicrobial drugs and metals encoded on a single mobile genetic element increases the probability of dissemination of these resistance determinants and the potential selection of multiple resistance mechanisms. In addition, the presence of a P7 entero-bacteriophage on the same plasmid, may represent a new vehicle for the propagation of TEM-116 in these soil communities. These findings highlight the role of the environment in the One Health initiative.
Collapse
Affiliation(s)
- Yashini Naidoo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria 0002, South Africa
| | - Angel Valverde
- Department of Microbial, Biochemical and Food Technology, University of the Free State, Nelson Mandela Drive, Bloemfontein 9300, South Africa
| | - Errol D Cason
- Department of Animal, Wildlife and Grassland Science, University of the Free State, Nelson Mandela Drive, Bloemfontein 9300, South Africa
| | - Rian E Pierneef
- Biotechnology Platform, Agricultural Research Council, Soutpan Road, Onderstepoort Campus, Pretoria 0110, South Africa
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria 0002, South Africa.
| |
Collapse
|
21
|
Filipic B, Novovic K, Studholme DJ, Malesevic M, Mirkovic N, Kojic M, Jovcic B. Shotgun metagenomics reveals differences in antibiotic resistance genes among bacterial communities in Western Balkans glacial lakes sediments. JOURNAL OF WATER AND HEALTH 2020; 18:383-397. [PMID: 32589623 DOI: 10.2166/wh.2020.227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Long-term overuse of antibiotics has driven the propagation and spreading of antibiotic resistance genes (ARGs) such as efflux pumps in the environment, which can be transferred to clinically relevant pathogens. This study explored the abundance and diversity of ARGs and mobile genetic elements within bacterial communities from sediments of three Western Balkans glacial lakes: Plav Lake (high impact of human population), Black Lake (medium impact of human population) and Donje Bare Lake (remote lake, minimal impact of human population) via shotgun metagenomics. Assembled metagenomic sequences revealed that Resistance-Nodulation-Division (RND) efflux pumps genes were most abundant in metagenome from the Plav Lake. The Integron Finder bioinformatics tool detected 38 clusters of attC sites lacking integron-integrases (CALIN) elements: 20 from Plav Lake, four from Black Lake and 14 from Donje Bare Lake. A complete integron sequence was recovered only from the assembled metagenome from Plav Lake. Plasmid contents within the metagenomes were similar, with proportions of contigs being plasmid-related: 1.73% for Plav Lake, 1.59% for Black Lake and 1.64% for Donje Bare Lake. The investigation showed that RNDs and mobile genetic elements content correlated with human population impact.
Collapse
Affiliation(s)
- Brankica Filipic
- Faculty of Pharmacy, University of Belgrade, Belgrade 11221, Serbia E-mail: ; Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11010, Serbia
| | - Katarina Novovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11010, Serbia
| | | | - Milka Malesevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11010, Serbia
| | - Nemanja Mirkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11010, Serbia
| | - Milan Kojic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11010, Serbia
| | - Branko Jovcic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11010, Serbia; Faculty of Biology, University of Belgrade, Belgrade 11000, Serbia
| |
Collapse
|
22
|
Staley ZR, Schmidt AM, Woodbury B, Eskridge KM, Durso L, Li X. Corn stalk residue may add antibiotic-resistant bacteria to manure composting piles. JOURNAL OF ENVIRONMENTAL QUALITY 2020; 49:745-753. [PMID: 33016408 DOI: 10.1002/jeq2.20017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/27/2019] [Indexed: 06/11/2023]
Abstract
Manure is commonly used as a fertilizer or soil conditioner; however, land application of untreated manure may introduce pathogens and antibiotic-resistant bacteria (ARB) into the soil, with harmful implications for public health. Composting is a manure management practice wherein a carbon-rich bulking agent, such as corn (Zea mays L.) stalk residue, is added to manure to achieve desirable carbon/nitrogen ratios to facilitate microbial activities and generate enough heat to inactivate pathogens, including antibiotic-resistant pathogens. However, when comparing compost piles and stockpiles for ARB reduction, we noticed that bulking agents added ARB to composting piles and compromised the performance of composting in reducing ARB. We hypothesized that ARB could be prevalent in corn stalk residues, a commonly used bulking agent for composting. To test this hypothesis, corn stalk residue samples throughout Nebraska were surveyed for the presence of ARB. Of the samples tested, 54% were positive for antibiotic-resistant Escherichia coli or enterococci using direct plating or after enrichment. Although not statistically significant, there was a trend wherein the use of pesticides tended to result in a greater prevalence of some ARB. Results from this study suggest that bulking agents can be a source of ARB in manure composting piles and highlight the importance of screening bulking agents for effective ARB reduction in livestock manure during composting.
Collapse
Affiliation(s)
- Zachery R Staley
- Dep. of Civil and Environmental Engineering, Univ. of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Amy Millmier Schmidt
- Dep. of Biological Systems Engineering, Univ. of Nebraska-Lincoln, Lincoln, NE, 68583, USA
- Dep. of Animal Science, Univ. of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Bryan Woodbury
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Kent M Eskridge
- Dep. of Statistics, Univ. of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Lisa Durso
- USDA-ARS, Lincoln, Lincoln, NE, 68583, USA
| | - Xu Li
- Dep. of Civil and Environmental Engineering, Univ. of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| |
Collapse
|
23
|
Yang Y, Ashworth AJ, Willett C, Cook K, Upadhyay A, Owens PR, Ricke SC, DeBruyn JM, Moore Jr. PA. Review of Antibiotic Resistance, Ecology, Dissemination, and Mitigation in U.S. Broiler Poultry Systems. Front Microbiol 2019; 10:2639. [PMID: 31803164 PMCID: PMC6872647 DOI: 10.3389/fmicb.2019.02639] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 10/30/2019] [Indexed: 12/24/2022] Open
Abstract
Since the onset of land application of poultry litter, transportation of microorganisms, antibiotics, and disinfectants to new locations has occurred. While some studies provide evidence that antimicrobial resistance (AMR), an evolutionary phenomenon, could be influenced by animal production systems, other research suggests AMR originates in the environment from non-anthropogenic sources. In addition, AMR impacts the effective prevention and treatment of poultry illnesses and is increasingly a threat to global public health. Therefore, there is a need to understand the dissemination of AMR genes to the environment, particularly those directly relevant to animal health using the One Health Approach. This review focuses on the potential movement of resistance genes to the soil via land application of poultry litter. Additionally, we highlight impacts of AMR on microbial ecology and explore hypotheses explaining gene movement pathways from U.S. broiler operations to the environment. Current approaches for decreasing antibiotic use in U.S. poultry operations are also described in this review.
Collapse
Affiliation(s)
- Yichao Yang
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Amanda J. Ashworth
- Poultry Production and Product Safety Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Fayetteville, AR, United States
| | - Cammy Willett
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Kimberly Cook
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Athens, GA, United States
| | - Abhinav Upadhyay
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Phillip R. Owens
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Dale Bumpers Small Farms Research Center, Booneville, AR, United States
| | - Steven C. Ricke
- Department of Food Science and Center for Food Safety, University of Arkansas, Fayetteville, AR, United States
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Philip A. Moore Jr.
- Poultry Production and Product Safety Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Fayetteville, AR, United States
| |
Collapse
|
24
|
Michalik A, Michalik K, Grzywacz B, Kalandyk-Kołodziejczyk M, Szklarzewicz T. Molecular characterization, ultrastructure, and transovarial transmission of Tremblaya phenacola in six mealybugs of the Phenacoccinae subfamily (Insecta, Hemiptera, Coccomorpha). PROTOPLASMA 2019; 256:1597-1608. [PMID: 31250115 PMCID: PMC6820616 DOI: 10.1007/s00709-019-01405-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 06/15/2019] [Indexed: 06/09/2023]
Abstract
Mealybugs (Hemiptera, Coccomorpha: Pseudococcidae) are plant sap-sucking insects which require close association with nutritional microorganisms for their proper development and reproduction. Here, we present the results of histological, ultrastructural, and molecular analyses of symbiotic systems of six mealybugs belonging to the Phenacoccinae subfamily: Phenacoccus aceris, Rhodania porifera, Coccura comari, Mirococcus clarus, Peliococcus calluneti, and Ceroputo pilosellae. Molecular analyses based on bacterial 16S rRNA genes have revealed that all the investigated species of Phenacoccinae are host to only one type of symbiotic bacteria-a large pleomorphic betaproteobacteria-Tremblaya phenacola. In all the species examined, bacteria are localized in the specialized cells of the host-insect termed bacteriocytes and are transovarially transmitted between generations. The mode of transovarial transmission is similar in all of the species investigated. Infection takes place in the neck region of the ovariole, between the tropharium and vitellarium. The co-phylogeny between mealybugs and bacteria Tremblaya has been also analyzed.
Collapse
Affiliation(s)
- Anna Michalik
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland.
| | - Katarzyna Michalik
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland
| | - Beata Grzywacz
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland
| | | | - Teresa Szklarzewicz
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland
| |
Collapse
|
25
|
Nnadozie CF, Odume ON. Freshwater environments as reservoirs of antibiotic resistant bacteria and their role in the dissemination of antibiotic resistance genes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:113067. [PMID: 31465907 DOI: 10.1016/j.envpol.2019.113067] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 05/12/2023]
Abstract
Freshwater environments are susceptible to possible contamination by residual antibiotics that are released through different sources, such as agricultural runoffs, sewage discharges and leaching from nearby farms. Freshwater environment can thus become reservoirs where an antibiotic impact microorganisms, and is an important public health concern. Degradation and dilution processes are fundamental for predicting the actual risk of antibiotic resistance dissemination from freshwater reservoirs. This study reviews major approaches for detecting and quantifying antibiotic resistance bacteria (ARBs) and genes (ARGs) in freshwater and their prevalence in these environments. Finally, the role of dilution, degradation, transmission and the persistence and fate of ARB/ARG in these environments are also reviewed. Culture-based single strain approaches and molecular techniques that include polymerase chain reaction (PCR), quantitative polymerase chain reaction (qPCR) and metagenomics are techniques for quantifying ARB and ARGs in freshwater environments. The level of ARBs is extremely high in most of the river systems (up to 98% of the total detected bacteria), followed by lakes (up to 77% of the total detected bacteria), compared to dam, pond, and spring (<1%). Of most concern is the occurrence of extended-spectrum β-lactamase producing Enterobacteriaceae, methicillin resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus (VRE), which cause highly epidemic infections. Dilution and natural degradation do not completely eradicate ARBs and ARGs in the freshwater environment. Even if the ARBs in freshwater are effectively inactivated by sunlight, their ARG-containing DNA can still be intact and capable of transferring resistance to non-resistant strains. Antibiotic resistance persists and is preserved in freshwater bodies polluted with high concentrations of antibiotics. Direct transmission of indigenous freshwater ARBs to humans as well as their transitory insertion in the microbiota can occur. These findings are disturbing especially for people that rely on freshwater resources for drinking, crop irrigation, and food in form of fish.
Collapse
Affiliation(s)
- Chika F Nnadozie
- Unilever Centre for Environmental Water Quality, Institute for Water Research, Rhodes University, PO Box 94, Grahamstown 6140, South Africa.
| | - Oghenekaro Nelson Odume
- Unilever Centre for Environmental Water Quality, Institute for Water Research, Rhodes University, PO Box 94, Grahamstown 6140, South Africa
| |
Collapse
|
26
|
Carvalho V, Freitas E, Fradinho J, Reis M, Oehmen A. The effect of seed sludge on the selection of a photo-EBPR system. N Biotechnol 2019; 49:112-119. [DOI: 10.1016/j.nbt.2018.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 10/10/2018] [Accepted: 10/20/2018] [Indexed: 10/28/2022]
|
27
|
Wu MS, Xu X. Inactivation of antibiotic-resistant bacteria by chlorine dioxide in soil and shifts in community composition. RSC Adv 2019; 9:6526-6532. [PMID: 35518509 PMCID: PMC9061123 DOI: 10.1039/c8ra07997h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/10/2019] [Indexed: 11/21/2022] Open
Abstract
Antibiotic-resistant bacteria are common widespread in soil and the most resistant species isStaphylococcus aureus.Sphingomonas,ArthrobacterandMassiliaare sensitive to ClO2.MicromonosporaceaeandThaumarchaeotaare more resistant to ClO2.
Collapse
Affiliation(s)
- M. S. Wu
- College of Resources and Civil Engineering
- Northeastern University
- Shenyang 100819
- China
- School of Resources and Materials
| | - X. Xu
- Tongji Zhejiang College
- Jiaxing
- China
| |
Collapse
|
28
|
Kenawy A, Dailin DJ, Abo-Zaid GA, Malek RA, Ambehabati KK, Zakaria KHN, Sayyed RZ, El Enshasy HA. Biosynthesis of Antibiotics by PGPR and Their Roles in Biocontrol of Plant Diseases. PLANT GROWTH PROMOTING RHIZOBACTERIA FOR SUSTAINABLE STRESS MANAGEMENT 2019:1-35. [DOI: 10.1007/978-981-13-6986-5_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
|
29
|
Qi X, Liu B, Wu H, Song Q, Jiang J, Bu Y, Rui J, Zou B, Zhou G. Bacterial communities under long-term conventional and transgenic cotton farming systems using V3-V5 and V5-V9 of 16s rDNA. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 164:618-628. [PMID: 30165339 DOI: 10.1016/j.ecoenv.2018.08.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/20/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
Abstract
Understanding the community structure of soil microbes is required to evaluate the potential effects of genetically modified (GM) plants on ecological environments. Bacterial communities in soil planted with conventional cotton (CC) and transgenic cultivar (TC) in a natural ecosystem for three years were characterized by 454 pyrosequencing of the V3-V5 and V5-V9 regions of 16S rDNA from June to September 2013. V3-V5 and V5-V9 regions yielded a total of 12,848 and 10,541 OTUs, respectively. The V5-V9 amplicon was additionally used to detect phyla that were poorly sequenced by V3-V5 (such as Chlamydiae, Crenarchaeota and Archaea). Among the species detected by each primer pair, 46% of the species identified from V3-V5 and 60% of those identified from V5-V9 were detected by both primer pairs. Although distinct bacterial compositions existed between the two amplified regions, statistical analysis revealed no significant difference in the diversity indexes or phylogenetic patterns in TC versus compared to those in the CC control. Further, clustering analysis in both regions indicated that there was no unambiguous aggregation in TC compared to that in CC control. Of all 26 phyla detected by both regions, each region detected 2 distinct phyla exhibiting significant variations in abundance. The species unique to each treatment field accounted for less than 27% of all species and were rare taxa (abundance < 0.15%). However, a small fraction of diagnostic taxa with specific ecological functions differed significantly between TC and CC. These differences were not driven by any obvious environmental factors. The results established a comprehensive inventory of the bacterial communities associated with GM plants and indicated that transgenic cotton may not significantly affect soil microorganisms compared with conventional cotton over a three-year period. Furthermore, diagnostic taxa were provided for monitoring the perturbation in soil, but further verification in future studies is required.
Collapse
Affiliation(s)
- Xiemin Qi
- Department of Pharmacology, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, School of Medicine, Nanjing University, Nanjing 210002, China
| | - Biao Liu
- Key Laboratory of Biosafety, Ministry of Environmental Protection of China, Nanjing Institute of Environmental Sciences, Nanjing 210042, China
| | - Haiping Wu
- Huadong Research Institute for Medicine and Biotechnics, Nanjing 210002, China
| | - Qinxin Song
- Department of Pharmacology, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, School of Medicine, Nanjing University, Nanjing 210002, China; Department of Pharmaceutical Analysis, Jiangsu key lab of drug screening, China Pharmaceutical University, Nanjing 210009, China
| | - Jingwei Jiang
- Department of Pharmaceutical Analysis, Jiangsu key lab of drug screening, China Pharmaceutical University, Nanjing 210009, China
| | - Ying Bu
- Huadong Research Institute for Medicine and Biotechnics, Nanjing 210002, China
| | - Jianzhong Rui
- Department of Pharmacology, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, School of Medicine, Nanjing University, Nanjing 210002, China
| | - Bingjie Zou
- Department of Pharmacology, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, School of Medicine, Nanjing University, Nanjing 210002, China.
| | - Guohua Zhou
- Department of Pharmacology, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, School of Medicine, Nanjing University, Nanjing 210002, China.
| |
Collapse
|
30
|
Michalik A, Szwedo J, Stroiński A, Świerczewski D, Szklarzewicz T. Symbiotic cornucopia of the monophagous planthopper Ommatidiotus dissimilis (Fallén, 1806) (Hemiptera: Fulgoromorpha: Caliscelidae). PROTOPLASMA 2018; 255:1317-1329. [PMID: 29516174 PMCID: PMC6133087 DOI: 10.1007/s00709-018-1234-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/26/2018] [Indexed: 05/31/2023]
Abstract
In contrast to Cicadomorpha, in which numerous symbiotic bacteria have been identified and characterized, the symbionts of fulgoromorphans are poorly known. Here, we present the results of histological, ultrastructural, and molecular analyses of the symbiotic system of the planthopper Ommatidiotus dissimilis. Amplification, cloning, and sequencing of bacterial 16S RNA genes have revealed that O. dissimilis is host to five types of bacteria. Apart from bacteria Sulcia and Vidania, which are regarded as ancestral symbionts of Fulgoromorpha, three additional types of bacteria belonging to the genera Sodalis, Wolbachia, and Rickettsia have been detected. Histological and ultrastructural investigations have shown that bacteria Sulcia, Vidania, and Sodalis house separate bacteriocytes, whereas bacteria Wolbachia and Rickettsia are dispersed within various insect tissue. Additionally, bacteria belonging to the genus Vidania occupy the bacteriome localized in the lumen of the hindgut. Both molecular and microscopic analyses have revealed that all the symbionts are transovarially transmitted between generations.
Collapse
Affiliation(s)
- Anna Michalik
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
| | - Jacek Szwedo
- Department of Invertebrate Zoology and Parasitology, University of Gdańsk, Wita Stwosza 59, 80-309 Gdańsk, Poland
| | - Adam Stroiński
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679 Warszawa, Poland
| | - Dariusz Świerczewski
- Department of Zoology and Animal Ecology, Jan Długosz University, Armii Krajowej 13/15, 42-201 Częstochowa, Poland
| | - Teresa Szklarzewicz
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
| |
Collapse
|
31
|
Carter DL, Docherty KM, Gill SA, Baker K, Teachout J, Vonhof MJ. Antibiotic resistant bacteria are widespread in songbirds across rural and urban environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:1234-1241. [PMID: 30857088 DOI: 10.1016/j.scitotenv.2018.01.343] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 05/20/2023]
Abstract
The widespread use of antibiotics in human and veterinary medicine to treat pathogenic bacteria has resulted in the rapid emergence of antibiotic-resistant bacteria (ARB). Wild animals may enable the spread of pathogenic and non-pathogenic ARB when they are exposed to reservoirs (e.g., contaminated soil, water, or crops) and carry ARB in and on their bodies to other environments. We tested for the presence of ARB in four songbird species in southwest Michigan across a gradient of land use. Our specific objectives were to: 1) quantify the prevalence of ARB found in the gut microbiome of birds; 2) identify the specific bacteria exhibiting resistance; 3) assess whether ARB prevalence and identity varied among bird species; and 4) assess whether anthropogenic land use influenced the prevalence and identity of ARB found on birds. We sampled birds across a land use gradient consisting of urban, agricultural, and natural land covers using a randomized, spatially-balanced sampling design and cultured bacteria from fecal samples in the presence of three different antibiotics (amoxicillin, tetracycline, and ciprofloxacin). Overall prevalence of ARB was high, with 88% of total birds carrying ARB resistant to one of three antibiotics that we tested. Resistance to amoxicillin was more common (83% of sampled birds) than resistance to tetracycline (15%) or ciprofloxacin (1%). Identified ARB were diverse, and included 135 isolates representing 5 bacterial phyla and 22 genera. There was no effect of land use on ARB prevalence, with 90% of sampled birds captured in rural sites and 85% of sampled birds in urban sites carrying ARB. We provide the first analysis of ARB prevalence across multiple bird species and land uses utilizing a spatially-balanced, randomized study design. Our results demonstrate that nearly all sampled birds carried at least some ARB, and that they may serve as important dispersal agents of ARB across large spatial scales.
Collapse
Affiliation(s)
- Diana L Carter
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Kathryn M Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Sharon A Gill
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Kathleen Baker
- Department of Geography, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Jordan Teachout
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Maarten J Vonhof
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States; Institute of the Environment and Sustainability, Western Michigan University, Kalamazoo, MI 49008, United States.
| |
Collapse
|
32
|
Pepper IL, Brooks JP, Gerba CP. Antibiotic Resistant Bacteria in Municipal Wastes: Is There Reason for Concern? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:3949-3959. [PMID: 29505255 DOI: 10.1021/acs.est.7b04360] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Recently, there has been increased concern about the presence of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARG), in treated domestic wastewaters, animal manures and municipal biosolids. The concern is whether these additional sources of ARB contribute to antibiotic resistance levels in the environment, that is, "environmental antibiotic resistance." ARB and ARG occur naturally in soil and water, and it remains unclear whether the introduction of ARB in liquid and solid municipal and animal wastes via land application have any significant impact on the background levels of antibiotic resistance in the environment, and whether they affect human exposure to ARB. In this current review, we examine and re-evaluate the incidence of ARB and ARG resulting from land application activities, and offer a new perspective on the threat of antibiotic resistance to public health via exposure from nonclinical environmental sources. Based on inputs of ARBs and ARGs from land application, their fate in soil due to soil microbial ecology principles, and background indigenous levels of ARBs and ARGs already present in soil, we conclude that while antibiotic resistance levels in soil are increased temporally by land application of wastes, their persistence is not guaranteed and is in fact variable, and often contradictory based on application site. Furthermore, the application of wastes may not produce the most direct impact of ARGs and ARB on public health. Further investigation is still warranted in agriculture and public health, including continued scrutiny of antibiotic use in both sectors.
Collapse
Affiliation(s)
- Ian L Pepper
- Water and Energy Sustainable Technology Center (WEST) , The University of Arizona , 2959 W. Calle Agua Nueva , Tucson , Arizona 85745 , United States
| | - John P Brooks
- Genetics and Sustainable Agriculture Research Unit, USDA ARS , Mississippi State , Mississippi , 39762 , United States
| | - Charles P Gerba
- Water and Energy Sustainable Technology Center (WEST) , The University of Arizona , 2959 W. Calle Agua Nueva , Tucson , Arizona 85745 , United States
| |
Collapse
|
33
|
Hily J, Demanèche S, Poulicard N, Tannières M, Djennane S, Beuve M, Vigne E, Demangeat G, Komar V, Gertz C, Marmonier A, Hemmer C, Vigneron S, Marais A, Candresse T, Simonet P, Lemaire O. Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:208-220. [PMID: 28544449 PMCID: PMC5785345 DOI: 10.1111/pbi.12761] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/12/2017] [Accepted: 05/19/2017] [Indexed: 06/07/2023]
Abstract
For some crops, the only possible approach to gain a specific trait requires genome modification. The development of virus-resistant transgenic plants based on the pathogen-derived resistance strategy has been a success story for over three decades. However, potential risks associated with the technology, such as horizontal gene transfer (HGT) of any part of the transgene to an existing gene pool, have been raised. Here, we report no evidence of any undesirable impacts of genetically modified (GM) grapevine rootstock on its biotic environment. Using state of the art metagenomics, we analysed two compartments in depth, the targeted Grapevine fanleaf virus (GFLV) populations and nontargeted root-associated microbiota. Our results reveal no statistically significant differences in the genetic diversity of bacteria that can be linked to the GM trait. In addition, no novel virus or bacteria recombinants of biosafety concern can be associated with transgenic grapevine rootstocks cultivated in commercial vineyard soil under greenhouse conditions for over 6 years.
Collapse
Affiliation(s)
| | - Sandrine Demanèche
- Laboratoire Ampère (CNRS UMR5005), Environmental Microbial GenomicsÉcole Centrale de LyonUniversité de LyonEcullyFrance
| | | | - Mélanie Tannières
- INRASVQV UMR‐A 1131Université de StrasbourgColmarFrance
- Present address:
European Biological Control LaboratoryUSDA‐ARSCampus International de Baillarguet CS 90013 Montferrier‐Sur‐Lez34988Saint Gely‐Du‐Fesc CedexFrance
| | | | - Monique Beuve
- INRASVQV UMR‐A 1131Université de StrasbourgColmarFrance
| | | | | | | | - Claude Gertz
- INRASVQV UMR‐A 1131Université de StrasbourgColmarFrance
| | | | | | | | - Armelle Marais
- UMR 1332 Biologie du Fruit et PathologieINRAUniversité de BordeauxVillenave d'Ornon CedexFrance
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et PathologieINRAUniversité de BordeauxVillenave d'Ornon CedexFrance
| | - Pascal Simonet
- Laboratoire Ampère (CNRS UMR5005), Environmental Microbial GenomicsÉcole Centrale de LyonUniversité de LyonEcullyFrance
| | | |
Collapse
|
34
|
Dan H, Ikeda N, Fujikami M, Nakabachi A. Behavior of bacteriome symbionts during transovarial transmission and development of the Asian citrus psyllid. PLoS One 2017; 12:e0189779. [PMID: 29240843 PMCID: PMC5730177 DOI: 10.1371/journal.pone.0189779] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/01/2017] [Indexed: 02/07/2023] Open
Abstract
The Asian citrus psyllid Diaphorina citri Kuwayama (Hemiptera: Liviidae) is a serious pest worldwide, transmitting Candidatus Liberibacter spp. (Alphaproteobacteria), the causative agents of a devastating citrus disease known as huanglongbing or greening disease. In a symbiotic organ called the bacteriome, D. citri possesses an organelle-like defensive symbiont, Candidatus Profftella armatura (Betaproteobacteria), and a nutritional symbiont, Ca. Carsonella ruddii (Gammaproteobacteria). Drastically reduced symbiont genomes and metabolic complementarity among the symbionts and D. citri indicate their mutually indispensable association. Moreover, horizontal gene transfer between the Profftella and Liberibacter lineages suggests ecological and evolutionary interactions between the bacteriome symbiont and the HLB pathogen. Using fluorescence in situ hybridization, we examined the behavior of Profftella and Carsonella during transovarial transmission and the development of D. citri. In the bacteriomes of sexually-mature female adults, symbionts transformed from an extremely elongated tubular form into spherical or short-rod forms, which migrated toward the ovary. The symbionts then formed mosaic masses, which entered at the posterior pole of the vitellogenic oocytes. After anatrepsis, Carsonella and Profftella migrated to the central and peripheral parts of the mass, respectively. Following the appearance of host nuclei, the mass cellularized, segregating Carsonella and Profftella in the central syncytium and peripheral uninucleate bacteriocytes, respectively. Subsequently, the uninucleate bacteriocytes harboring Profftella assembled at the posterior pole, while the syncytium, containing Carsonella, sat on the anterior side facing the germ band initiating katatrepsis. During dorsal closure, the syncytium was divided into uninuclear bacteriocytes, which surrounded the mass of bacteriocytes containing Profftella. Once fully surrounded, the bacteriocyte mass containing Profftella was fused into a syncytium. Prior to hatching, a pair of wing-like protrusions arose from both lateral sides of the bacteriome, which continued to grow throughout the nymphal stages. These findings provide a foundation for better understanding the intricate relationship between D. citri and its microbiota.
Collapse
Affiliation(s)
- Hiroki Dan
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Naoya Ikeda
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Masaya Fujikami
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Atsushi Nakabachi
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi, Japan
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, Toyohashi, Aichi, Japan
| |
Collapse
|
35
|
Nazir R, Shen JP, Wang JT, Hu HW, He JZ. Fungal networks serve as novel ecological routes for enrichment and dissemination of antibiotic resistance genes as exhibited by microcosm experiments. Sci Rep 2017; 7:15457. [PMID: 29133838 PMCID: PMC5684214 DOI: 10.1038/s41598-017-15660-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 10/31/2017] [Indexed: 11/09/2022] Open
Abstract
Antibiotic resistance genes (ARGs) in the environment and their subsequent acquisition by clinically important microorganisms are a serious concern. However, the spread of environmental ARGs remain largely unknown. We report, for the first time, the involvement of soil fungi in the distribution of bacteria with ARGs via soil microcosms. qPCR assay detected unique ARGs specifically found in the mycosphere of different fungi. Interestingly, the taxonomically and ecologically different fungi exerted different selection pressures on ARGs originating from the same source. Test fungi supported different antibiotic resistance bacteria enriched in the mycosphere and even transported to distant places. The relative abundance of the tnpA gene decreased, for manure, along mycelial networks of all fungi. While the fungal strain NFC-5 enriched the intI1 gene more, opposite to two other fungi at the migration front compared with the inoculation point for both sources. Such data indicate the differential effect of different fungi to facilitate horizontal gene transfer potential under fungal selection pressure. Our study provides the evidence that fungi can contribute ARGs, host bacterial diversity and abundance, and such interactive microbial consortia have the potential to disseminate the resistance determinants from one place to another, thus increasing the ARGs exposure risk to humans.
Collapse
Affiliation(s)
- Rashid Nazir
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, 22060, Pakistan
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China. .,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| |
Collapse
|
36
|
Polymorphism of antibiotic-inactivating enzyme driven by ecology expands the environmental resistome. ISME JOURNAL 2017; 12:267-276. [PMID: 29028006 DOI: 10.1038/ismej.2017.168] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/10/2017] [Accepted: 08/14/2017] [Indexed: 12/15/2022]
Abstract
The environmental resistome has been recognized as the origin and reservoir of antibiotic resistance genes and considered to be dynamic and ever expanding. In this study, a targeted gene sequencing approach revealed that the polymorphic diversity of the aminoglycoside-inactivating enzyme AAC(6')-Ib was ecological niche-specific. AAC(6')-Ib-cr, previously known as a clinical variant, was prevalent in various soils and the intestines of chickens and humans, suggesting that this variant might not have arisen from adaptive mutations in the clinic but instead originated from the environment. Furthermore, ecologically dominant polymorphic variants of AAC(6')-Ib were characterized and found to display different substrate specificities for quinolones and aminoglycosides, conferring the altered resistance spectra. Interestingly, a novel variant with the D179Y substitution showed an extended resistance spectrum to the recently developed fluoroquinolone gemifloxacin. Our results suggest that soil and animal microbiomes could be major reservoirs of antibiotic resistance; polymorphic diversity expands the antibiotic resistome in the environment, resulting in the potential emergence of novel resistance.
Collapse
|
37
|
Wang C, Dong D, Strong PJ, Zhu W, Ma Z, Qin Y, Wu W. Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes. MICROBIOME 2017; 5:103. [PMID: 28814344 PMCID: PMC5559795 DOI: 10.1186/s40168-017-0324-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 08/07/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases. In this study, changes of resistome expression were determined and related to active microbiome profiles during the dynamic composting process. This was achieved by integrating metagenomic and time series metatranscriptomic data for the evolving microbial community during composting. RESULTS Composting noticeably reduced the aggregated expression level of the manure resistome, which primarily consisted of genes encoding for tetracycline, vancomycin, fluoroquinolone, beta-lactam, and aminoglycoside resistance, as well as efflux pumps. Furthermore, a varied transcriptional response of resistome to composting at the ARG levels was highlighted. The expression of tetracycline resistance genes (tetM-tetW-tetO-tetS) decreased during composting, where distinctive shifts in the four phases of composting were related to variations in antibiotic concentration. Composting had no effect on the expression of sulfonamide and fluoroquinolone resistance genes, which increased slightly during the thermophilic phase and then decreased to initial levels. As indigenous populations switched greatly throughout the dynamic composting, the core resistome persisted and their reservoir hosts' composition was significantly correlated with dynamic active microbial phylogenetic structure. Hosts for sulfonamide and fuoroquinolone resistance genes changed notably in phylognetic structure and underwent an initial increase and then a decrease in abundance. By contrast, hosts for tetracycline resistance genes (tetM-tetW-tetO-tetS) exhibited a constant decline through time. CONCLUSIONS The transcriptional patterns of a core resistome over the course of composting were identified, and microbial phylogeny was the key determinant in defining the varied transcriptional response of resistome to this dynamic biological process. This research demonstrated the benefits of composting for manure treatment. It reduced the risk of emerging environmental contaminants such as tetracyclines, tetracycline resistance genes, and clinically relevant pathogens carrying ARGs, as well as RNA viruses and bacteriophages.
Collapse
Affiliation(s)
- Cheng Wang
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Da Dong
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration, Zhejiang A & F University, Lin’an, 311300 China
| | - P. J. Strong
- Queensland University of Technology, GPO Box 2432, 2 George St, Brisbane, QLD 4001 Australia
| | - Weijing Zhu
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Zhuang Ma
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Yong Qin
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Weixiang Wu
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| |
Collapse
|
38
|
Food Waste to Energy: An Overview of Sustainable Approaches for Food Waste Management and Nutrient Recycling. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2370927. [PMID: 28293629 PMCID: PMC5331173 DOI: 10.1155/2017/2370927] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/29/2016] [Accepted: 01/12/2017] [Indexed: 01/06/2023]
Abstract
Food wastage and its accumulation are becoming a critical problem around the globe due to continuous increase of the world population. The exponential growth in food waste is imposing serious threats to our society like environmental pollution, health risk, and scarcity of dumping land. There is an urgent need to take appropriate measures to reduce food waste burden by adopting standard management practices. Currently, various kinds of approaches are investigated in waste food processing and management for societal benefits and applications. Anaerobic digestion approach has appeared as one of the most ecofriendly and promising solutions for food wastes management, energy, and nutrient production, which can contribute to world's ever-increasing energy requirements. Here, we have briefly described and explored the different aspects of anaerobic biodegrading approaches for food waste, effects of cosubstrates, effect of environmental factors, contribution of microbial population, and available computational resources for food waste management researches.
Collapse
|
39
|
Differential detection of pathogenic Yersinia spp. by fluorescence in situ hybridization. Food Microbiol 2016; 62:39-45. [PMID: 27889163 DOI: 10.1016/j.fm.2016.09.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 09/16/2016] [Accepted: 09/18/2016] [Indexed: 12/12/2022]
Abstract
Yersinia enterocolitica, Y. pseudotuberculosis and Y. pestis are pathogens of major medical importance, which are responsible for a considerable number of infections every year. The detection of these species still relies on cultural methods, which are slow, labour intensive and often hampered by the presence of high amounts of accompanying flora. In this study, fluorescence in situ hybridization (FISH) was used to develop a fast, sensitive and reliable alternative to detect viable bacteria in food. For this purpose, highly specific probes targeting the 16S and 23S ribosomal RNA were employed to differentially detect each of the three species. In order to enable the differentiation of single nucleotide polymorphisms (SNPs), suitable competitor oligonucleotides and locked nucleic acids (LNAs) were used. Starved cells still showed a strong signal and a direct viable count (DVC) approach combined with FISH optimized live/dead discrimination. Sensitivity of the FISH test was high and even a single cell per gram of spiked minced pork meat could be detected within a day, demonstrating the applicability to identify foodborne hazards at an early stage. In conclusion, the established FISH tests proved to be promising tools to compensate existing drawbacks of the conventional cultural detection of these important zoonotic agents.
Collapse
|
40
|
Pagaling E, Gatica J, Yang K, Cytryn E, Yan T. Phylogenetic diversity of ceftriaxone resistance and the presence of extended-spectrum β-lactamase genes in the culturable soil resistome. J Glob Antimicrob Resist 2016; 6:128-135. [DOI: 10.1016/j.jgar.2016.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/22/2016] [Accepted: 05/30/2016] [Indexed: 11/29/2022] Open
|
41
|
Laffite A, Kilunga PI, Kayembe JM, Devarajan N, Mulaji CK, Giuliani G, Slaveykova VI, Poté J. Hospital Effluents Are One of Several Sources of Metal, Antibiotic Resistance Genes, and Bacterial Markers Disseminated in Sub-Saharan Urban Rivers. Front Microbiol 2016; 7:1128. [PMID: 27499749 PMCID: PMC4956658 DOI: 10.3389/fmicb.2016.01128] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
Data concerning the occurrence of emerging biological contaminants such as antibiotic resistance genes (ARGs) and fecal indicator bacteria (FIB) in aquatic environments in Sub-Saharan African countries is limited. On the other hand, antibiotic resistance remains a worldwide problem which may pose serious potential risks to human and animal health. Consequently, there is a growing number of reports concerning the prevalence and dissemination of these contaminants into various environmental compartments. Sediments provide the opportunity to reconstruct the pollution history and evaluate impacts so this study investigates the abundance and distribution of toxic metals, FIB, and ARGs released from hospital effluent wastewaters and their presence in river sediments receiving systems. ARGs (bla TEM, bla CTX-M, bla SHV, and aadA), total bacterial load, and selected bacterial species FIB [Escherichia coli, Enterococcus (ENT)] and species (Psd) were quantified by targeting species specific genes using quantitative PCR (qPCR) in total DNA extracted from the sediments recovered from 4 hospital outlet pipes (HOP) and their river receiving systems in the City of Kinshasa in the Democratic Republic of the Congo. The results highlight the great concentration of toxic metals in HOP, reaching the values (in mg kg(-1)) of 47.9 (Cr), 213.6 (Cu), 1434.4 (Zn), 2.6 (Cd), 281.5 (Pb), and 13.6 (Hg). The results also highlight the highest (P < 0.05) values of 16S rRNA, FIB, and ARGs copy numbers in all sampling sites including upstream (control site), discharge point, and downstream of receiving rivers, indicating that the hospital effluent water is not an exclusive source of the biological contaminants entering the urban rivers. Significant correlation were observed between (i) all analyzed ARGs and total bacterial load (16S rRNA) 0.51 to 0.72 (p < 0.001, n = 65); (ii) ARGs (except bla TEM) and FIB and Psd 0.57 < r < 0.82 (p < 0.001, n = 65); and (iii) ARGs (except bla TEM) and toxic metals (Cd, Cr, Cu, and Zn) 0.44 to 0.72, (p < 0.001, n = 65). These findings demonstrate that several sources including hospital and urban wastewaters contribute to the spread of toxic metals and biological emerging contaminants in aquatic ecosystems.
Collapse
Affiliation(s)
- Amandine Laffite
- Faculty of Science, Earth and Environmental Science Section, F.-A. Forel Institute and Institute of Environmental Sciences, University of Geneva Geneva, Switzerland
| | - Pitchouna I Kilunga
- Department of Chemistry, Faculty of Science, University of Kinshasa Kinshasa, Democratic Republic of the Congo
| | - John M Kayembe
- Département de Géographie-Science de l'Environnement, Faculté des Sciences, Université Pédagogique Nationale Kinshasa, Democratic Republic of the Congo
| | - Naresh Devarajan
- Faculty of Science, Earth and Environmental Science Section, F.-A. Forel Institute and Institute of Environmental Sciences, University of Geneva Geneva, Switzerland
| | - Crispin K Mulaji
- Department of Chemistry, Faculty of Science, University of Kinshasa Kinshasa, Democratic Republic of the Congo
| | - Gregory Giuliani
- Faculty of Science, Earth and Environmental Science Section, F.-A. Forel Institute and Institute of Environmental Sciences, University of GenevaGeneva, Switzerland; enviroSPACE Lab., Institute for Environmental Sciences, University of GenevaGeneva, Switzerland; United Nations Environment Programme, Division of Early Warning and Assessment, Global Resource Information Database - Geneva, International Environment HouseGeneva, Switzerland
| | - Vera I Slaveykova
- Faculty of Science, Earth and Environmental Science Section, F.-A. Forel Institute and Institute of Environmental Sciences, University of Geneva Geneva, Switzerland
| | - John Poté
- Faculty of Science, Earth and Environmental Science Section, F.-A. Forel Institute and Institute of Environmental Sciences, University of GenevaGeneva, Switzerland; Department of Chemistry, Faculty of Science, University of KinshasaKinshasa, Democratic Republic of the Congo; Département de Géographie-Science de l'Environnement, Faculté des Sciences, Université Pédagogique NationaleKinshasa, Democratic Republic of the Congo
| |
Collapse
|
42
|
Borges A, Abreu AC, Dias C, Saavedra MJ, Borges F, Simões M. New Perspectives on the Use of Phytochemicals as an Emergent Strategy to Control Bacterial Infections Including Biofilms. Molecules 2016; 21:molecules21070877. [PMID: 27399652 PMCID: PMC6274140 DOI: 10.3390/molecules21070877] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 02/07/2023] Open
Abstract
The majority of current infectious diseases are almost untreatable by conventional antibiotic therapy given the advent of multidrug-resistant bacteria. The degree of severity and the persistence of infections are worsened when microorganisms form biofilms. Therefore, efforts are being applied to develop new drugs not as vulnerable as the current ones to bacterial resistance mechanisms, and also able to target bacteria in biofilms. Natural products, especially those obtained from plants, have proven to be outstanding compounds with unique properties, making them perfect candidates for these much-needed therapeutics. This review presents the current knowledge on the potentialities of plant products as antibiotic adjuvants to restore the therapeutic activity of drugs. Further, the difficulties associated with the use of the existing antibiotics in the treatment of biofilm-related infections are described. To counteract the biofilm resistance problems, innovative strategies are suggested based on literature data. Among the proposed strategies, the use of phytochemicals to inhibit or eradicate biofilms is highlighted. An overview on the use of phytochemicals to interfere with bacterial quorum sensing (QS) signaling pathways and underlying phenotypes is provided. The use of phytochemicals as chelating agents and efflux pump inhibitors is also reviewed.
Collapse
Affiliation(s)
- Anabela Borges
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, Porto 4200-465, Portugal.
- CIQUP, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal.
- CECAV-Veterinary and Animal Science Research Center, Department of Veterinary Science, University of Trás-os-Montes e Alto Douro, Apartado 1013, Vila Real 5001-801, Portugal.
| | - Ana Cristina Abreu
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, Porto 4200-465, Portugal.
- CECAV-Veterinary and Animal Science Research Center, Department of Veterinary Science, University of Trás-os-Montes e Alto Douro, Apartado 1013, Vila Real 5001-801, Portugal.
| | - Carla Dias
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, Porto 4200-465, Portugal.
- CECAV-Veterinary and Animal Science Research Center, Department of Veterinary Science, University of Trás-os-Montes e Alto Douro, Apartado 1013, Vila Real 5001-801, Portugal.
| | - Maria José Saavedra
- CECAV-Veterinary and Animal Science Research Center, Department of Veterinary Science, University of Trás-os-Montes e Alto Douro, Apartado 1013, Vila Real 5001-801, Portugal.
| | - Fernanda Borges
- CIQUP, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal.
| | - Manuel Simões
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, Porto 4200-465, Portugal.
| |
Collapse
|
43
|
Durso LM, Wedin DA, Gilley JE, Miller DN, Marx DB. Assessment of Selected Antibiotic Resistances in Ungrazed Native Nebraska Prairie Soils. JOURNAL OF ENVIRONMENTAL QUALITY 2016; 45:454-62. [PMID: 27065391 DOI: 10.2134/jeq2015.06.0280] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The inherent spatial heterogeneity and complexity of antibiotic-resistant bacteria and antibiotic resistance (AR) genes in manure-affected soils makes it difficult to sort out resistance that can be attributed to human antibiotic use from resistance that occurs naturally in the soil. This study characterizes native Nebraska prairie soils that have not been affected by human or food-animal waste products to provide data on background levels of resistance in southeastern Nebraskan soils. Soil samples were collected from 20 sites enumerated on tetracycline and cefotaxime media; screened for tetracycline-, sulfonamide-, β-lactamase-, and macrolide-resistance genes; and characterized for soil physical and chemical parameters. All prairies contained tetracycline- and cefotaxime-resistant bacteria, and 48% of isolates collected were resistant to two or more antibiotics. Most (98%) of the soil samples and all 20 prairies had at least one tetracycline gene. Most frequently detected were (D), (A) (O), (L), and (B). Sulfonamide genes, which are considered a marker of human or animal activity, were detected in 91% of the samples, despite the lack of human inputs at these sites. No correlations were found between either phenotypic or genotypic resistance and soil physical or chemical parameters. Heterogeneity was observed in AR within and between prairies. Therefore, multiple samples are necessary to overcome heterogeneity and to accurately assess AR. Conclusions regarding AR depend on the gene target measured. To determine the impacts of food-animal antibiotic use on resistance, it is essential that background and/or baseline levels be considered, and where appropriate subtracted out, when evaluating AR in agroecosystems.
Collapse
|
44
|
Rothrock MJ, Keen PL, Cook KL, Durso LM, Franklin AM, Dungan RS. How Should We Be Determining Background and Baseline Antibiotic Resistance Levels in Agroecosystem Research? JOURNAL OF ENVIRONMENTAL QUALITY 2016; 45:420-431. [PMID: 27065388 DOI: 10.2134/jeq2015.06.0327] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Although historically, antibiotic resistance has occurred naturally in environmental bacteria, many questions remain regarding the specifics of how humans and animals contribute to the development and spread of antibiotic resistance in agroecosystems. Additional research is necessary to completely understand the potential risks to human, animal, and ecological health in systems altered by antibiotic-resistance-related contamination. At present, analyzing and interpreting the effects of human and animal inputs on antibiotic resistance in agroecosystems is difficult, since standard research terminology and protocols do not exist for studying background and baseline levels of resistance in the environment. To improve the state of science in antibiotic-resistance-related research in agroecosystems, researchers are encouraged to incorporate baseline data within the study system and background data from outside the study system to normalize the study data and determine the potential impact of antibiotic-resistance-related determinants on a specific agroecosystem. Therefore, the aims of this review were to (i) present standard definitions for commonly used terms in environmental antibiotic resistance research and (ii) illustrate the need for research standards (normalization) within and between studies of antibiotic resistance in agroecosystems. To foster synergy among antibiotic resistance researchers, a new surveillance and decision-making tool is proposed to assist researchers in determining the most relevant and important antibiotic-resistance-related targets to focus on in their given agroecosystems. Incorporation of these components within antibiotic-resistance-related studies should allow for a more comprehensive and accurate picture of the current and future states of antibiotic resistance in the environment.
Collapse
|
45
|
Devarajan N, Laffite A, Mulaji CK, Otamonga JP, Mpiana PT, Mubedi JI, Prabakar K, Ibelings BW, Poté J. Occurrence of Antibiotic Resistance Genes and Bacterial Markers in a Tropical River Receiving Hospital and Urban Wastewaters. PLoS One 2016; 11:e0149211. [PMID: 26910062 PMCID: PMC4766091 DOI: 10.1371/journal.pone.0149211] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/28/2016] [Indexed: 12/21/2022] Open
Abstract
The occurrence of emerging biological contaminants including antibiotic resistance genes (ARGs) and Faecal Indicator Bacteria (FIB) is still little investigated in developing countries under tropical conditions. In this study, the total bacterial load, the abundance of FIB (E. coli and Enterococcus spp. (ENT)), Pseudomonas spp. and ARGs (blaTEM, blaCTX-M, blaSHV, blaNDM and aadA) were quantified using quantitative PCR in the total DNA extracted from the sediments recovered from hospital outlet pipes (HOP) and the Cauvery River Basin (CRB), Tiruchirappalli, Tamil Nadu, India. The abundance of bacterial marker genes were 120, 104 and 89 fold higher for the E. coli, Enterococcus spp. and Pseudomonas spp., respectively at HOP when compared with CRB. The ARGs aadA and blaTEM were most frequently detected in higher concentration than other ARGs at all the sampling sites. The ARGs blaSHV and blaNDM were identified in CRB sediments contaminated by hospital and urban wastewaters. The ARGs abundance strongly correlated (r ≥ 0.36, p < 0.05, n = 45) with total bacterial load and E. coli in the sediments, indicating a common origin and extant source of contamination. Tropical aquatic ecosystems receiving wastewaters can act as reservoir of ARGs, which could potentially be transferred to susceptible bacterial pathogens at these sites.
Collapse
Affiliation(s)
- Naresh Devarajan
- University of Geneva, Institute F. A. Forel and Institute of Environmental Sciences, Geneva, Switzerland
| | - Amandine Laffite
- University of Geneva, Institute F. A. Forel and Institute of Environmental Sciences, Geneva, Switzerland
| | - Crispin Kyela Mulaji
- University of Kinshasa (UNIKIN), Faculty of Science, Department of Chemistry, Kinshasa XI, Democratic Republic of the Congo
| | - Jean-Paul Otamonga
- Université Pédagogique Nationale (UPN), Croisement Route de Matadi et Avenue de la Libération, Quartier Binza/UPN, Kinshasa, Democratic Republic of the Congo
| | - Pius Tshimankinda Mpiana
- University of Kinshasa (UNIKIN), Faculty of Science, Department of Chemistry, Kinshasa XI, Democratic Republic of the Congo
| | - Josué Ilunga Mubedi
- Université Pédagogique Nationale (UPN), Croisement Route de Matadi et Avenue de la Libération, Quartier Binza/UPN, Kinshasa, Democratic Republic of the Congo
| | - Kandasamy Prabakar
- Postgraduate and Research Department of Zoology, Jamal Mohamed College, Tiruchirappalli-620020, Tamil Nadu, India
| | - Bastiaan Willem Ibelings
- University of Geneva, Institute F. A. Forel and Institute of Environmental Sciences, Geneva, Switzerland
| | - John Poté
- University of Geneva, Institute F. A. Forel and Institute of Environmental Sciences, Geneva, Switzerland
- University of Kinshasa (UNIKIN), Faculty of Science, Department of Chemistry, Kinshasa XI, Democratic Republic of the Congo
- Université Pédagogique Nationale (UPN), Croisement Route de Matadi et Avenue de la Libération, Quartier Binza/UPN, Kinshasa, Democratic Republic of the Congo
| |
Collapse
|
46
|
Hu HW, Han XM, Shi XZ, Wang JT, Han LL, Chen D, He JZ. Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure. FEMS Microbiol Ecol 2015; 92:fiv169. [DOI: 10.1093/femsec/fiv169] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2015] [Indexed: 02/07/2023] Open
|
47
|
Takeshita K, Matsuura Y, Itoh H, Navarro R, Hori T, Sone T, Kamagata Y, Mergaert P, Kikuchi Y. Burkholderia of Plant-Beneficial Group are Symbiotically Associated with Bordered Plant Bugs (Heteroptera: Pyrrhocoroidea: Largidae). Microbes Environ 2015; 30:321-9. [PMID: 26657305 PMCID: PMC4676555 DOI: 10.1264/jsme2.me15153] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A number of phytophagous stinkbugs (order Heteroptera: infraorder Pentatomomorpha) harbor symbiotic bacteria in a specific midgut region composed of numerous crypts. Among the five superfamilies of the infraorder Pentatomomorpha, most members of the Coreoidea and Lygaeoidea are associated with a specific group of the genus Burkholderia, called the “stinkbug-associated beneficial and environmental (SBE)” group, which is not vertically transmitted, but acquired from the environment every host generation. A recent study reported that, in addition to these two stinkbug groups, the family Largidae of the superfamily Pyrrhocoroidea also possesses a Burkholderia symbiont. Despite this recent finding, the phylogenetic position and biological nature of Burkholderia associated with Largidae remains unclear. Based on the combined results of fluorescence in situ hybridization, cloning analysis, Illumina deep sequencing, and egg inspections by diagnostic PCR, we herein demonstrate that the largid species are consistently associated with the “plant-associated beneficial and environmental (PBE)” group of Burkholderia, which are phylogenetically distinct from the SBE group, and that they maintain symbiosis through the environmental acquisition of the bacteria. Since the superfamilies Coreoidea, Lygaeoidea, and Pyrrhocoroidea are monophyletic in the infraorder Pentatomomorpha, it is plausible that the symbiotic association with Burkholderia evolved at the common ancestor of the three superfamilies. However, the results of this study strongly suggest that a dynamic transition from the PBE to SBE group, or vice versa, occurred in the course of stinkbug evolution.
Collapse
|
48
|
Woegerbauer M, Zeinzinger J, Gottsberger RA, Pascher K, Hufnagl P, Indra A, Fuchs R, Hofrichter J, Kopacka I, Korschineck I, Schleicher C, Schwarz M, Steinwider J, Springer B, Allerberger F, Nielsen KM, Fuchs K. Antibiotic resistance marker genes as environmental pollutants in GMO-pristine agricultural soils in Austria. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2015; 206:342-351. [PMID: 26232739 DOI: 10.1016/j.envpol.2015.07.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 07/15/2015] [Accepted: 07/18/2015] [Indexed: 06/04/2023]
Abstract
Antibiotic resistance genes may be considered as environmental pollutants if anthropogenic emission and manipulations increase their prevalence above usually occurring background levels. The prevalence of aph(3')-IIa/nptII and aph(3')-IIIa/nptIII - frequent marker genes in plant biotechnology conferring resistance to certain aminoglycosides - was determined in Austrian soils from 100 maize and potato fields not yet exposed to but eligible for GMO crop cultivation. Total soil DNA extracts were analysed by nptII/nptIII-specific TaqMan real time PCR. Of all fields 6% were positive for nptII (median: 150 copies/g soil; range: 31-856) and 85% for nptIII (1190 copies/g soil; 13-61600). The copy-number deduced prevalence of nptIII carriers was 14-fold higher compared to nptII. Of the cultivable kanamycin-resistant soil bacteria 1.8% (95% confidence interval: 0-3.3%) were positive for nptIII, none for nptII (0-0.8%). The nptII-load of the studied soils was low rendering nptII a typical candidate as environmental pollutant upon anthropogenic release into these ecosystems.
Collapse
Affiliation(s)
- Markus Woegerbauer
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria.
| | - Josef Zeinzinger
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Richard Alexander Gottsberger
- Division for Food Security, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Kathrin Pascher
- Department of Integrative Biology and Biodiversity Research (DIB), Institute of Zoology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Hufnagl
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Alexander Indra
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Reinhard Fuchs
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Johannes Hofrichter
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Ian Kopacka
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | | | - Corina Schleicher
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Michael Schwarz
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Johann Steinwider
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Burkhard Springer
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Franz Allerberger
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Kaare M Nielsen
- GenØk - Centre for Biosafety and Department of Pharmacy, University of Tromsø, Norway
| | - Klemens Fuchs
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| |
Collapse
|
49
|
Devarajan N, Laffite A, Graham ND, Meijer M, Prabakar K, Mubedi JI, Elongo V, Mpiana PT, Ibelings BW, Wildi W, Poté J. Accumulation of clinically relevant antibiotic-resistance genes, bacterial load, and metals in freshwater lake sediments in Central Europe. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:6528-6537. [PMID: 25933054 DOI: 10.1021/acs.est.5b01031] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Wastewater treatment plants (WWTP) receive the effluents from various sources (communities, industrial, and hospital effluents) and are recognized as reservoir for antibiotic-resistance genes (ARGs) that are associated with clinical pathogens. The aquatic environment is considered a hot-spot for horizontal gene transfer, and lake sediments offer the opportunity for reconstructing the pollution history and evaluating the impacts. In this context, variation with depth and time of the total bacterial load, the abundance of faecal indicator bacteria (FIB; E. coli and Enterococcus spp. (ENT)), Pseudomonas spp., and ARGs (blaTEM, blaSHV, blaCTX-M, blaNDM, and aadA) were quantified in sediment profiles of different parts of Lake Geneva using quantitative PCR. The abundance of bacterial marker genes was identified in sediments contaminated by WWTP following eutrophication of the lake. Additionally, ARGs, including the extended-spectrum ß-lactam- and aminoglycoside-resistance genes, were identified in the surface sediments. The ARG and FIB abundance strongly correlated (r ≥ 0.403, p < 0.05, n = 34) with organic matter and metal concentrations in the sediments, indicating a common and contemporary source of contamination. The contamination of sediments by untreated or partially treated effluent water can affect the quality of ecosystem. Therefore, the reduction of contaminants from the source is recommended for further improvement of water quality.
Collapse
Affiliation(s)
- Naresh Devarajan
- †University of Geneva, Faculty of Sciences, Earth and Environmental Sciences, Institute F. A. Forel and Institute of Environmental Sciences, Case Postale 416, 1290 Versoix, Switzerland
| | - Amandine Laffite
- †University of Geneva, Faculty of Sciences, Earth and Environmental Sciences, Institute F. A. Forel and Institute of Environmental Sciences, Case Postale 416, 1290 Versoix, Switzerland
| | - Neil D Graham
- †University of Geneva, Faculty of Sciences, Earth and Environmental Sciences, Institute F. A. Forel and Institute of Environmental Sciences, Case Postale 416, 1290 Versoix, Switzerland
| | - Maria Meijer
- †University of Geneva, Faculty of Sciences, Earth and Environmental Sciences, Institute F. A. Forel and Institute of Environmental Sciences, Case Postale 416, 1290 Versoix, Switzerland
| | - Kandasamy Prabakar
- ‡Postgraduate and Research Department of Zoology, Jamal Mohamed College, Tiruchirappalli, 620020 Tamil Nadu, India
| | - Josué I Mubedi
- §Université Pédagogique Nationale, Croisement Route de Matadi et Avenue de la Libération, Quartier Binza/UPN, Boı̂te Postale 8815, Kinshasa, République Démocratique du Congo
| | - Vicky Elongo
- ∥Université de Kinshasa, Faculté des Lettres et Sciences Humaines, Département des Sciences de l'Information et de la Communication, Boı̂te Postale 243, Kinshasa XI, République Démocratique du Congo
| | - Pius T Mpiana
- ⊥University of Kinshasa, Faculty of Science, Department of Chemistry, Boı̂te Postale 190, Kinshasa XI, Democratic Republic of the Congo
| | - Bastiaan Willem Ibelings
- †University of Geneva, Faculty of Sciences, Earth and Environmental Sciences, Institute F. A. Forel and Institute of Environmental Sciences, Case Postale 416, 1290 Versoix, Switzerland
| | - Walter Wildi
- †University of Geneva, Faculty of Sciences, Earth and Environmental Sciences, Institute F. A. Forel and Institute of Environmental Sciences, Case Postale 416, 1290 Versoix, Switzerland
| | - John Poté
- †University of Geneva, Faculty of Sciences, Earth and Environmental Sciences, Institute F. A. Forel and Institute of Environmental Sciences, Case Postale 416, 1290 Versoix, Switzerland
- §Université Pédagogique Nationale, Croisement Route de Matadi et Avenue de la Libération, Quartier Binza/UPN, Boı̂te Postale 8815, Kinshasa, République Démocratique du Congo
- ⊥University of Kinshasa, Faculty of Science, Department of Chemistry, Boı̂te Postale 190, Kinshasa XI, Democratic Republic of the Congo
| |
Collapse
|
50
|
Nesme J, Simonet P. The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria. Environ Microbiol 2014; 17:913-30. [DOI: 10.1111/1462-2920.12631] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 09/15/2014] [Accepted: 09/19/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Joseph Nesme
- Environmental Microbial Genomics, Bioengineering Departement, Laboratoire Ampère, CNRS UMR5005, Ecole Centrale de Lyon; Université de Lyon; 36 Avenue Guy de Collongue Ecully 69134 France
| | - Pascal Simonet
- Environmental Microbial Genomics, Bioengineering Departement, Laboratoire Ampère, CNRS UMR5005, Ecole Centrale de Lyon; Université de Lyon; 36 Avenue Guy de Collongue Ecully 69134 France
| |
Collapse
|