1
|
Santamarina-García G, Amores G, Llamazares D, Hernández I, Javier R Barron L, Virto M. Phenotypic and genotypic characterization of antimicrobial resistances reveals the effect of the production chain in reducing resistant lactic acid bacteria in an artisanal raw ewe milk PDO cheese. Food Res Int 2024; 187:114308. [PMID: 38763625 DOI: 10.1016/j.foodres.2024.114308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/27/2024] [Accepted: 04/16/2024] [Indexed: 05/21/2024]
Abstract
Antimicrobial resistance (AMR) is a significant public health threat, with the food production chain, and, specifically, fermented products, as a potential vehicle for dissemination. However, information about dairy products, especially raw ewe milk cheeses, is limited. The present study analysed, for the first time, the occurrence of AMRs related to lactic acid bacteria (LAB) along a raw ewe milk cheese production chain for the most common antimicrobial agents used on farms (dihydrostreptomycin, benzylpenicillin, amoxicillin and polymyxin B). More than 200 LAB isolates were obtained and identified by Sanger sequencing (V1-V3 16S rRNA regions); these isolates included 8 LAB genera and 21 species. Significant differences in LAB composition were observed throughout the production chain (P ≤ 0.001), with Enterococcus (e.g., E. hirae and E. faecalis) and Bacillus (e.g., B. thuringiensis and B. cereus) predominating in ovine faeces and raw ewe milk, respectively, along with Lactococcus (L. lactis) in whey and fresh cheeses, while Lactobacillus and Lacticaseibacillus species (e.g., Lactobacillus sp. and L. paracasei) prevailed in ripened cheeses. Phenotypically, by broth microdilution, Lactococcus, Enterococcus and Bacillus species presented the greatest resistance rates (on average, 78.2 %, 56.8 % and 53.4 %, respectively), specifically against polymyxin B, and were more susceptible to dihydrostreptomycin. Conversely, Lacticaseibacillus and Lactobacillus were more susceptible to all antimicrobials tested (31.4 % and 39.1 %, respectively). Thus, resistance patterns and multidrug resistance were reduced along the production chain (P ≤ 0.05). Genotypically, through HT-qPCR, 31 antimicrobial resistance genes (ARGs) and 6 mobile genetic elements (MGEs) were detected, predominating Str, StrB and aadA-01, related to aminoglycoside resistance, and the transposons tnpA-02 and tnpA-01. In general, a significant reduction in ARGs and MGEs abundances was also observed throughout the production chain (P ≤ 0.001). The current findings indicate that LAB dynamics throughout the raw ewe milk cheese production chain facilitated a reduction in AMRs, which has not been reported to date.
Collapse
Affiliation(s)
- Gorka Santamarina-García
- Lactiker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba Health Research Institute-Prevention, Promotion and Health Care, 01009 Vitoria-Gasteiz, Spain; Joint Research Laboratory on Environmental Antibiotic Resistance, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
| | - Gustavo Amores
- Lactiker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba Health Research Institute-Prevention, Promotion and Health Care, 01009 Vitoria-Gasteiz, Spain; Joint Research Laboratory on Environmental Antibiotic Resistance, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Diego Llamazares
- Lactiker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Igor Hernández
- Lactiker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba Health Research Institute-Prevention, Promotion and Health Care, 01009 Vitoria-Gasteiz, Spain; Joint Research Laboratory on Environmental Antibiotic Resistance, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Luis Javier R Barron
- Lactiker Research Group, Department of Pharmacy and Food Sciences, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Joint Research Laboratory on Environmental Antibiotic Resistance, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Mailo Virto
- Lactiker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba Health Research Institute-Prevention, Promotion and Health Care, 01009 Vitoria-Gasteiz, Spain; Joint Research Laboratory on Environmental Antibiotic Resistance, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| |
Collapse
|
2
|
Alkorta I, Garbisu C. Expanding the focus of the One Health concept: links between the Earth-system processes of the planetary boundaries framework and antibiotic resistance. REVIEWS ON ENVIRONMENTAL HEALTH 2024; 0:reveh-2024-0013. [PMID: 38815132 DOI: 10.1515/reveh-2024-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/26/2024] [Indexed: 06/01/2024]
Abstract
The scientific community warns that our impact on planet Earth is so acute that we are crossing several of the planetary boundaries that demarcate the safe operating space for humankind. Besides, there is mounting evidence of serious effects on people's health derived from the ongoing environmental degradation. Regarding human health, the spread of antibiotic resistant bacteria is one of the most critical public health issues worldwide. Relevantly, antibiotic resistance has been claimed to be the quintessential One Health issue. The One Health concept links human, animal, and environmental health, but it is frequently only focused on the risk of zoonotic pathogens to public health or, to a lesser extent, the impact of contaminants on human health, i.e., adverse effects on human health coming from the other two One Health "compartments". It is recurrently claimed that antibiotic resistance must be approached from a One Health perspective, but such statement often only refers to the connection between the use of antibiotics in veterinary practice and the antibiotic resistance crisis, or the impact of contaminants (antibiotics, heavy metals, disinfectants, etc.) on antibiotic resistance. Nonetheless, the nine Earth-system processes considered in the planetary boundaries framework can be directly or indirectly linked to antibiotic resistance. Here, some of the main links between those processes and the dissemination of antibiotic resistance are described. The ultimate goal is to expand the focus of the One Health concept by pointing out the links between critical Earth-system processes and the One Health quintessential issue, i.e., antibiotic resistance.
Collapse
Affiliation(s)
- Itziar Alkorta
- Department of Biochemistry and Molecular Biology, 16402 University of the Basque Country (UPV/EHU) , Bilbao, Spain
| | - Carlos Garbisu
- NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
| |
Collapse
|
3
|
Lupolt SN, Kim BF, Agnew J, Ramachandran G, Burke TA, Kennedy RD, Nachman KE. Application and demonstration of meso-activity exposure factors to advance estimates of incidental soil ingestion among agricultural workers. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2024:10.1038/s41370-024-00671-0. [PMID: 38760534 DOI: 10.1038/s41370-024-00671-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Soil is an understudied and underregulated pathway of chemical exposure, particularly for agricultural workers who cultivate food in soils. Little is known about how agricultural workers spend their time and how they may contact soil while growing food. Exposure factors are behavioral and environmental variables used in exposure estimation. OBJECTIVES Our study aimed to derive exposure factors describing how growers engage in different tasks and use those factors to advance the use of time-activity data to estimate soil ingestion exposures among agricultural workers. METHODS We administered a meso-activity-based, season-specific soil contact activity questionnaire to 38 fruit and vegetable growers. We asked growers to estimate the frequency and duration of six meso-activities and describe how they completed them. We used questionnaire data to derive exposure factors and estimate empirical and simulated exposures to a hypothetical contaminant in soil via incidental ingestion using daily, hourly, and hourly-task-specific ingestion rates. RESULTS We generated exposure factors characterizing the frequency and duration of six meso-activities by season, and self-reported soil contact, glove use, and handwashing practices by meso-activity and season. Seasonal average daily doses (ADDs) were similar across all three forms of ingestion rates. No consistent patterns regarding task-specific contributions to seasonal or annual ADDs were observed.
Collapse
Affiliation(s)
- Sara N Lupolt
- Department of Environmental Health & Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Johns Hopkins Center for a Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Risk Sciences and Public Policy Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Brent F Kim
- Department of Environmental Health & Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Johns Hopkins Center for a Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jacqueline Agnew
- Department of Environmental Health & Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Gurumurthy Ramachandran
- Department of Environmental Health & Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Thomas A Burke
- Risk Sciences and Public Policy Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ryan David Kennedy
- Department of Health Behavior and Society, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Keeve E Nachman
- Department of Environmental Health & Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Johns Hopkins Center for a Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Risk Sciences and Public Policy Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| |
Collapse
|
4
|
Li T, Tao S, Ma M, Liu S, Shen M, Zhang H. Is the application of organic fertilizers becoming an undeniable source of microplastics and resistance genes in agricultural systems? THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169571. [PMID: 38142997 DOI: 10.1016/j.scitotenv.2023.169571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/04/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
The application of organic fertilizers is becoming an undeniable source of microplastics and antibiotic resistance genes (ARGs) in agricultural soils. The complex microbial activity further transfers resistance genes and their host bacteria to agricultural products and throughout the entire food chain. Therefore, the current main focus is on reducing the abundance of microplastics and ARGs in organic fertilizers at the source, as well as managing microplastics and ARGs in soil. The control of microplastic abundance in organic fertilizers is currently only achieved through pre-composting selection and other methods. However, there are still many shortcomings in the research on the distribution characteristics, propagation and diffusion mechanisms, and control technologies of ARGs, and some key scientific issues still need to be urgently addressed. The high-temperature composting of organic waste can effectively reduce the abundance of ARGs in organic fertilizers to a certain extent. However, it is also important to consider the spread of ARGs in residual antibiotic-resistant bacteria (ARB). This article systematically explores the pathways and interactions of microplastics and resistance genes entering agricultural soils through the application of organic fertilizers. The removal of microplastics and ARGs from organic fertilizers was discussed in detail. Based on the limitations of existing research, further investigation in this area is expected to provide valuable insights for the development and practical implementation of technologies aimed at reducing soil microplastics and resistance genes.
Collapse
Affiliation(s)
- Tianhao Li
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui 243002, PR China
| | - Shiyu Tao
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui 243002, PR China
| | - Mengjie Ma
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui 243002, PR China
| | - Shiwei Liu
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui 243002, PR China
| | - Maocai Shen
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui 243002, PR China.
| | - Huijuan Zhang
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui 243002, PR China.
| |
Collapse
|
5
|
Ajayi AO, Odeyemi AT, Akinjogunla OJ, Adeyeye AB, Ayo-ajayi I. Review of antibiotic-resistant bacteria and antibiotic resistance genes within the one health framework. Infect Ecol Epidemiol 2024; 14:2312953. [PMID: 38371518 PMCID: PMC10868463 DOI: 10.1080/20008686.2024.2312953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Background: The interdisciplinary One Health (OH) approach recognizes that human, animal, and environmental health are all interconnected. Its ultimate goal is to promote optimal health for all through the exploration of these relationships. Antibiotic resistance (AR) is a public health challenge that has been primarily addressed within the context of human health and clinical settings. However, it has become increasingly evident that antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) that confer resistance are transmitted and circulated within humans, animals, and the environment. Therefore, to effectively address this issue, antibiotic resistance must also be considered an environmental and livestock/wildlife problem. Objective: This review was carried out to provide a broad overview of the existence of ARB and ARGs in One Health settings. Methods: Relevant studies that placed emphasis on ARB and ARGs were reviewed and key findings were accessed that illustrate the importance of One Health as a measure to tackle growing public and environmental threats. Results: In this review, we delve into the complex interplay of the three components of OH in relation to ARB and ARGs. Antibiotics used in animal husbandry and plants to promote growth, treat, and prevent infectious diseases lead to the development of antibiotic-resistant bacteria in animals. These bacteria are transmitted from animals to humans through food and environmental exposure. The environment plays a critical role in the circulation and persistence of antibiotic-resistant bacteria and genes, posing a significant threat to human and animal health. This article also highlights how ARGs are spread in the environment through the transfer of genetic material between bacteria. This transfer can occur naturally or through human activities such as the use of antibiotics in agriculture and waste management practices. Conclusion: It is important to integrate the One Health approach into the public health system to effectively tackle the emergence and spread of ARB and genes that code for resistance to different antibiotics.
Collapse
Affiliation(s)
| | - Adebowale Toba Odeyemi
- Department of Microbiology, Landmark University SDG Groups 2 and 3, Omu-Aran, Kwara State, Nigeria
| | | | | | - Ibiwumi Ayo-ajayi
- Department of Computer Science, Afe Babalola University, Ado Ekiti, Ekiti State, Nigeria
| |
Collapse
|
6
|
Gama GSP, Pimenta AS, Feijó FMC, de Azevedo TKB, de Melo RR, de Andrade GS. The Potential of Wood Vinegar to Replace Antimicrobials Used in Animal Husbandry-A Review. Animals (Basel) 2024; 14:381. [PMID: 38338024 PMCID: PMC10854697 DOI: 10.3390/ani14030381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/16/2023] [Accepted: 12/27/2023] [Indexed: 02/12/2024] Open
Abstract
The indiscriminate use of antimicrobials in animal husbandry can result in various types of environmental contamination. Part of the dose of these products is excreted, still active, in the animals' feces and urine. These excreta are widely used as organic fertilizers, which results in contamination with antimicrobial molecules. The impacts can occur in several compartments, such as soil, groundwater, and surface watercourses. Also, contamination by antimicrobials fed or administrated to pigs, chickens, and cattle can reach the meat, milk, and other animal products, which calls into question the sustainability of using these products as part of eco-friendly practices. Therefore, a search for alternative natural products is required to replace the conventional antimicrobials currently used in animal husbandry, aiming to mitigate environmental contamination. We thus carried out a review addressing this issue, highlighting wood vinegar (WV), also known as pyroligneous acid, as an alternative antimicrobial with good potential to replace conventional products. In this regard, many studies have demonstrated that WV is a promising product. WV is a nontoxic additive widely employed in the food industry to impart a smoked flavor to foods. Studies have shown that, depending on the WV concentration, good results can be achieved using it as an antimicrobial against pathogenic bacteria and fungi and a valuable growth promoter for poultry and pigs.
Collapse
Affiliation(s)
- Gil Sander Próspero Gama
- Graduate Program in Forest Sciences, Forest Engineering, Universidade Federal do Rio Grande do Norte, Rodovia RN 160, km 03 s/n, Distrito de Jundiaí, Macaíba CEP 59.280-000, Brazil; (G.S.P.G.); (A.S.P.); (T.K.B.d.A.); (G.S.d.A.)
| | - Alexandre Santos Pimenta
- Graduate Program in Forest Sciences, Forest Engineering, Universidade Federal do Rio Grande do Norte, Rodovia RN 160, km 03 s/n, Distrito de Jundiaí, Macaíba CEP 59.280-000, Brazil; (G.S.P.G.); (A.S.P.); (T.K.B.d.A.); (G.S.d.A.)
| | - Francisco Marlon Carneiro Feijó
- Graduate Program in Environment, Technology, and Society—PPGATS, Laboratory of Veterinary Microbiology and Laboratory of Wood Technology, Universidade Federal Rural do Semiárido—UFERSA, Av. Francisco Mota, 572—Bairro Costa e Silva, Mossoró CEP 59.625-900, Brazil;
| | - Tatiane Kelly Barbosa de Azevedo
- Graduate Program in Forest Sciences, Forest Engineering, Universidade Federal do Rio Grande do Norte, Rodovia RN 160, km 03 s/n, Distrito de Jundiaí, Macaíba CEP 59.280-000, Brazil; (G.S.P.G.); (A.S.P.); (T.K.B.d.A.); (G.S.d.A.)
| | - Rafael Rodolfo de Melo
- Graduate Program in Environment, Technology, and Society—PPGATS, Laboratory of Veterinary Microbiology and Laboratory of Wood Technology, Universidade Federal Rural do Semiárido—UFERSA, Av. Francisco Mota, 572—Bairro Costa e Silva, Mossoró CEP 59.625-900, Brazil;
| | - Gabriel Siqueira de Andrade
- Graduate Program in Forest Sciences, Forest Engineering, Universidade Federal do Rio Grande do Norte, Rodovia RN 160, km 03 s/n, Distrito de Jundiaí, Macaíba CEP 59.280-000, Brazil; (G.S.P.G.); (A.S.P.); (T.K.B.d.A.); (G.S.d.A.)
| |
Collapse
|
7
|
Jampani M, Mateo-Sagasta J, Chandrasekar A, Fatta-Kassinos D, Graham DW, Gothwal R, Moodley A, Chadag VM, Wiberg D, Langan S. Fate and transport modelling for evaluating antibiotic resistance in aquatic environments: Current knowledge and research priorities. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132527. [PMID: 37788551 DOI: 10.1016/j.jhazmat.2023.132527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 08/03/2023] [Accepted: 09/09/2023] [Indexed: 10/05/2023]
Abstract
Antibiotics have revolutionised medicine in the last century and enabled the prevention of bacterial infections that were previously deemed untreatable. However, in parallel, bacteria have increasingly developed resistance to antibiotics through various mechanisms. When resistant bacteria find their way into terrestrial and aquatic environments, animal and human exposures increase, e.g., via polluted soil, food, and water, and health risks multiply. Understanding the fate and transport of antibiotic resistant bacteria (ARB) and the transfer mechanisms of antibiotic resistance genes (ARGs) in aquatic environments is critical for evaluating and mitigating the risks of resistant-induced infections. The conceptual understanding of sources and pathways of antibiotics, ARB, and ARGs from society to the water environments is essential for setting the scene and developing an appropriate framework for modelling. Various factors and processes associated with hydrology, ecology, and climate change can significantly affect the fate and transport of ARB and ARGs in natural environments. This article reviews current knowledge, research gaps, and priorities for developing water quality models to assess the fate and transport of ARB and ARGs. The paper also provides inputs on future research needs, especially the need for new predictive models to guide risk assessment on AR transmission and spread in aquatic environments.
Collapse
Affiliation(s)
- Mahesh Jampani
- International Water Management Institute (IWMI), Battaramulla, Colombo, Sri Lanka.
| | - Javier Mateo-Sagasta
- International Water Management Institute (IWMI), Battaramulla, Colombo, Sri Lanka
| | - Aparna Chandrasekar
- UFZ - Helmholtz Centre for Environmental Research, Department Computational Hydrosystems, Leipzig, Germany; Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Despo Fatta-Kassinos
- Civil and Environmental Engineering Department and Nireas International Water Research Center, University of Cyprus, Nicosia, Cyprus
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Ritu Gothwal
- International Water Management Institute (IWMI), Battaramulla, Colombo, Sri Lanka
| | - Arshnee Moodley
- International Livestock Research Institute (ILRI), Nairobi, Kenya; Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | | | - David Wiberg
- International Water Management Institute (IWMI), Battaramulla, Colombo, Sri Lanka
| | - Simon Langan
- International Water Management Institute (IWMI), Battaramulla, Colombo, Sri Lanka
| |
Collapse
|
8
|
Arbé-Carton K, Rey-Sogo A, Santos-Fernández N, Altube O, Garbisu C, Arana L, Alkorta I. Development of a high-throughput platform to measure plasmid transfer frequency. Front Cell Infect Microbiol 2023; 13:1269732. [PMID: 37886666 PMCID: PMC10598849 DOI: 10.3389/fcimb.2023.1269732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Antibiotic resistance represents one of the greatest threats to global health. The spread of antibiotic resistance genes among bacteria occurs mostly through horizontal gene transfer via conjugation mediated by plasmids. This process implies a direct contact between a donor and a recipient bacterium which acquires the antibiotic resistance genes encoded by the plasmid and, concomitantly, the capacity to transfer the acquired plasmid to a new recipient. Classical assays for the measurement of plasmid transfer frequency (i.e., conjugation frequency) are often characterized by a high variability and, hence, they require many biological and technical replicates to reduce such variability and the accompanying uncertainty. In addition, classical conjugation assays are commonly tedious and time-consuming because they typically involve counting colonies on a large number of plates for the quantification of donors, recipients, and transconjugants (i.e., the bacteria that have received the genetic material by conjugation). Due to the magnitude of the antibiotic resistance problem, it is critical to develop reliable and rapid methods for the quantification of plasmid transfer frequency that allow the simultaneous analysis of many samples. Here, we present the development of a high-throughput, reliable, quick, easy, and cost-effective method to simultaneously accomplish and measure multiple conjugation events in 96-well plates, in which the quantification of donors, recipients, and transconjugants is estimated from the time required to reach a specific threshold value (OD600 value) in the bacterial growth curves. Our method successfully discriminates different plasmid transfer frequencies, yielding results that are equivalent to those obtained by a classical conjugation assay.
Collapse
Affiliation(s)
- Kepa Arbé-Carton
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Ana Rey-Sogo
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Nagore Santos-Fernández
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Oihane Altube
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Carlos Garbisu
- Department of Conservation of Natural Resources, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Lide Arana
- Department of Applied Chemistry, University of the Basque Country (UPV/EHU), Donostia, Spain
| | - Itziar Alkorta
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| |
Collapse
|
9
|
Tarabai H, Krejci S, Karyakin I, Bitar I, Literak I, Dolejska M. Clinically relevant antibiotic resistance in Escherichia coli from black kites in southwestern Siberia: a genetic and phenotypic investigation. mSphere 2023; 8:e0009923. [PMID: 37310717 PMCID: PMC10449506 DOI: 10.1128/msphere.00099-23] [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: 02/24/2023] [Accepted: 04/27/2023] [Indexed: 06/14/2023] Open
Abstract
Wild birds including raptors can act as vectors of clinically relevant bacteria with antibiotic resistance. The aim of this study was to investigate the occurrence of antibiotic-resistant Escherichia coli in black kites (Milvus migrans) inhabiting localities in proximity to human-influenced environments in southwestern Siberia and investigate their virulence and plasmid contents. A total of 51 E. coli isolates mostly with multidrug resistance (MDR) profiles were obtained from cloacal swabs of 35 (64%, n = 55) kites. Genomic analyses of 36 whole genome sequenced E. coli isolates showed: (i) high prevalence and diversity of their antibiotic resistance genes (ARGs) and common association with ESBL/AmpC production (27/36, 75%), (ii) carriage of mcr-1 for colistin resistance on IncI2 plasmids in kites residing in proximity of two large cities, (iii) frequent association with class one integrase (IntI1, 22/36, 61%), and (iv) presence of sequence types (STs) linked to avian-pathogenic (APEC) and extra-intestinal pathogenic E. coli (ExPEC). Notably, numerous isolates had significant virulence content. One E. coli with APEC-associated ST354 carried qnrE1 encoding fluoroquinolone resistance on IncHI2-ST3 plasmid, the first detection of such a gene in E. coli from wildlife. Our results implicate black kites in southwestern Siberia as reservoirs for antibiotic-resistant E. coli. It also highlights the existing link between proximity of wildlife to human activities and their carriage of MDR bacteria including pathogenic STs with significant and clinically relevant antibiotic resistance determinants. IMPORTANCE Migratory birds have the potential to acquire and disperse clinically relevant antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs) through vast geographical regions. The opportunistic feeding behavior associated with some raptors including black kites and the growing anthropogenic influence on their natural habitats increase the transmission risk of multidrug resistance (MDR) and pathogenic bacteria from human and agricultural sources into the environment and wildlife. Thus, monitoring studies investigating antibiotic resistance in raptors may provide essential data that facilitate understanding the fate and evolution of ARB and ARGs in the environment and possible health risks for humans and animals associated with the acquisition of these resistance determinants by wildlife.
Collapse
Affiliation(s)
- Hassan Tarabai
- Central European Institute of Technology (CEITEC), University of Veterinary Sciences, Brno, Czech Republic
- Department of Parasitology, Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Simon Krejci
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences, Brno, Czech Republic
| | | | - Ibrahim Bitar
- Biomedical Center, Charles University, Prague, Czech Republic
| | - Ivan Literak
- Central European Institute of Technology (CEITEC), University of Veterinary Sciences, Brno, Czech Republic
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences, Brno, Czech Republic
| | - Monika Dolejska
- Central European Institute of Technology (CEITEC), University of Veterinary Sciences, Brno, Czech Republic
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences, Brno, Czech Republic
- Biomedical Center, Charles University, Prague, Czech Republic
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital, Brno, Czech Republic
| |
Collapse
|
10
|
Kardava K, Tetz V, Vecherkovskaya M, Tetz G. Seed dressing with M451 promotes seedling growth in wheat and reduces root phytopathogenic fungi without affecting endophytes. FRONTIERS IN PLANT SCIENCE 2023; 14:1176553. [PMID: 37265634 PMCID: PMC10229829 DOI: 10.3389/fpls.2023.1176553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/17/2023] [Indexed: 06/03/2023]
Abstract
Fungal plant infections result in substantial losses to the agricultural sector. A range of fungicide seed dressings are available to control seed-borne fungal diseases; however, they lack sufficient efficacy because of intrinsic tolerance and acquired resistance. Moreover, many fungicide seed dressings can also penetrate plants, negatively affecting plant growth owing to their toxic effects on endophytes, as well as contributing to the spread of antibiotic resistance. Here, we evaluated the efficacy of M451, a member of a new class of antimicrobial agents that are not relevant to human healthcare. As a seed dressing for wheat seeds, M451 exhibited significant antifungal activity against one of the most devastating plant fungal pathogens, Fusarium spp. Furthermore, M451 was more active than the commercially used fungicide Maxim XL against both seed-borne and soil-borne F. oxysporum infection. Importantly, and unlike other antifungals, M451 seed dressing did not inhibit any of the major characteristics of wheat grains and seedlings, such as germination percentage, germination time, grain vigor, shoot- and root weight and length, but rather improved some of these parameters. The results also demonstrated that M451 had no negative impacts on endophytes and did not accumulate in grains. Thus, M451 may have potential applications as an antifungal agent in wheat cultivation.
Collapse
Affiliation(s)
| | | | | | - G. Tetz
- Department of Systems Biology, Human Microbiology Institute, New York, NY, United States
| |
Collapse
|
11
|
Marutescu LG. Current and Future Flow Cytometry Applications Contributing to Antimicrobial Resistance Control. Microorganisms 2023; 11:1300. [PMID: 37317273 DOI: 10.3390/microorganisms11051300] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023] Open
Abstract
Antimicrobial resistance is a global threat to human health and welfare, food safety, and environmental health. The rapid detection and quantification of antimicrobial resistance are important for both infectious disease control and public health threat assessment. Technologies such as flow cytometry can provide clinicians with the early information, they need for appropriate antibiotic treatment. At the same time, cytometry platforms facilitate the measurement of antibiotic-resistant bacteria in environments impacted by human activities, enabling assessment of their impact on watersheds and soils. This review focuses on the latest applications of flow cytometry for the detection of pathogens and antibiotic-resistant bacteria in both clinical and environmental samples. Novel antimicrobial susceptibility testing frameworks embedding flow cytometry assays can contribute to the implementation of global antimicrobial resistance surveillance systems that are needed for science-based decisions and actions.
Collapse
Affiliation(s)
- Luminita Gabriela Marutescu
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, 91-95 Spl. Independentei, 050095 Bucharest, Romania
- Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| |
Collapse
|
12
|
Yang F, Shen S, Gao W, Ma Y, Han B, Ding Y, Wang X, Zhang K. Deciphering discriminative antibiotic resistance genes and pathogens in agricultural soil following chemical and organic fertilizer. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 322:116110. [PMID: 36049303 DOI: 10.1016/j.jenvman.2022.116110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/17/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Fertilizers containing rich nutrients can change the profiles of antibiotic resistant pathogens (ARPs) and antibiotic resistance genes (ARGs) in receiving soils; however, the discriminative ARGs and ARPs in agricultural soil following different fertilizer applications remain unknown. Using metagenomic sequencing combined with binning approach, the present study investigated the discriminative ARGs and ARPs under various fertilizer applications (chemical and organic fertilizer) in a 8-year field experiment. VanR, multidrug ARG transporter, vanS, ermA, and arnA were the discriminative ARGs in the chemical fertilizer group, whereas rosB, multidrug transporter, mexW, and aac(3)-I were enhanced in the organic fertilizer group. The metagenomic binning approach revealed that both fertilizer applications caused pathogen proliferation. Chemical fertilizer caused the increase in the pathogenic genus Luteimonas, and organic fertilizer facilitated the proliferation of the pathogenic genera Dokdonella and Pseudomonas. The pathogenic species Pseudomonas_H sp014836765, carrying mexW and multidrug transporter, was enriched only in the organic fertilizer group, indicating that it was a discriminative ARP in the organic fertilizer group. Our results demonstrated that fertilizer application, particularly organic fertilizer application, can facilitate the proliferation of ARGs and ARPs in the receiving soil, posing the risk of the development and spread of soil-borne ARPs.
Collapse
Affiliation(s)
- Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, 671004, China
| | - Shizhou Shen
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, 671004, China
| | - Wenxuan Gao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, 671004, China
| | - Yingjun Ma
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yongzhen Ding
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Xiaolong Wang
- School of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China.
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, 671004, China.
| |
Collapse
|
13
|
Marutescu LG, Jaga M, Postolache C, Barbuceanu F, Milita NM, Romascu LM, Schmitt H, de Roda Husman AM, Sefeedpari P, Glaeser S, Kämpfer P, Boerlin P, Topp E, Gradisteanu Pircalabioru G, Chifiriuc MC, Popa M. Insights into the impact of manure on the environmental antibiotic residues and resistance pool. Front Microbiol 2022; 13:965132. [PMID: 36187968 PMCID: PMC9522911 DOI: 10.3389/fmicb.2022.965132] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
The intensive use of antibiotics in the veterinary sector, linked to the application of manure-derived amendments in agriculture, translates into increased environmental levels of chemical residues, AR bacteria (ARB) and antibiotic resistance genes (ARG). The aim of this review was to evaluate the current evidence regarding the impact of animal farming and manure application on the antibiotic resistance pool in the environment. Several studies reported correlations between the prevalence of clinically relevant ARB and the amount and classes of antibiotics used in animal farming (high resistance rates being reported for medically important antibiotics such as penicillins, tetracyclines, sulfonamides and fluoroquinolones). However, the results are difficult to compare, due to the diversity of the used antimicrobials quantification techniques and to the different amounts and types of antibiotics, exhibiting various degradation times, given in animal feed in different countries. The soils fertilized with manure-derived products harbor a higher and chronic abundance of ARB, multiple ARG and an enriched associated mobilome, which is also sometimes seen in the crops grown on the amended soils. Different manure processing techniques have various efficiencies in the removal of antibiotic residues, ARB and ARGs, but there is only a small amount of data from commercial farms. The efficiency of sludge anaerobic digestion appears to be dependent on the microbial communities composition, the ARB/ARG and operating temperature (mesophilic vs. thermophilic conditions). Composting seems to reduce or eliminate most of antibiotics residues, enteric bacteria, ARB and different representative ARG in manure more rapidly and effectively than lagoon storage. Our review highlights that despite the body of research accumulated in the last years, there are still important knowledge gaps regarding the contribution of manure to the AMR emergence, accumulation, spread and risk of human exposure in countries with high clinical resistance rates. Land microbiome before and after manure application, efficiency of different manure treatment techniques in decreasing the AMR levels in the natural environments and along the food chain must be investigated in depth, covering different geographical regions and countries and using harmonized methodologies. The support of stakeholders is required for the development of specific best practices for prudent – cautious use of antibiotics on farm animals. The use of human reserve antibiotics in veterinary medicine and of unprescribed animal antimicrobials should be stopped and the use of antibiotics on farms must be limited. This integrated approach is needed to determine the optimal conditions for the removal of antibiotic residues, ARB and ARG, to formulate specific recommendations for livestock manure treatment, storage and handling procedures and to translate them into practical on-farm management decisions, to ultimately prevent exposure of human population.
Collapse
Affiliation(s)
- Luminita Gabriela Marutescu
- Department of Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of University of Bucharest, Bucharest, Romania
| | - Mihaela Jaga
- Department of Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | | | - Florica Barbuceanu
- Research Institute of University of Bucharest, Bucharest, Romania
- The Institute for Diagnostic and Animal Health (IDSA), Bucharest, Romania
- Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Bucharest, Romania
| | - Nicoleta Manuela Milita
- Research Institute of University of Bucharest, Bucharest, Romania
- The Institute for Diagnostic and Animal Health (IDSA), Bucharest, Romania
- Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Bucharest, Romania
| | - Luminita Maria Romascu
- Research Institute of University of Bucharest, Bucharest, Romania
- The Institute for Diagnostic and Animal Health (IDSA), Bucharest, Romania
- Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Bucharest, Romania
| | - Heike Schmitt
- National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | | | | | - Stefanie Glaeser
- Institute for Applied Microbiology Heinrich-Buff-Ring, Justus-Liebig University, Gießen, Germany
| | - Peter Kämpfer
- Institute for Applied Microbiology Heinrich-Buff-Ring, Justus-Liebig University, Gießen, Germany
| | - Patrick Boerlin
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Edward Topp
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Department of Biology, Agriculture and Agri-Food Canada, University of Western Ontario, London, ON, Canada
| | - Gratiela Gradisteanu Pircalabioru
- Department of Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of University of Bucharest, Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
- *Correspondence: Gratiela Gradisteanu Pircalabioru,
| | - Mariana Carmen Chifiriuc
- Department of Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of University of Bucharest, Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
- The Romanian Academy, Bucharest, Romania
- Mariana Carmen Chifiriuc,
| | - Marcela Popa
- Department of Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of University of Bucharest, Bucharest, Romania
| |
Collapse
|
14
|
Qing L, Qigen D, Jian H, Hongjun W, Jingdu C. Profiles of tetracycline resistance genes in paddy soils with three different organic fertilizer applications. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119368. [PMID: 35489540 DOI: 10.1016/j.envpol.2022.119368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/01/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
The rapid expansion of organic rice cultivation areas have been accompanied by increased application of organic fertilizers. The high prevalence of soil antibiotic resistance caused by organic fertilizer application poses a severe threat to the agricultural and soil ecosystems. To date, research efforts and understanding of the effects and mechanism of action of the various organic fertilizers on antibiotic resistance in paddy soils remain poorly investigated. Tetracycline resistance genes (TRGs, including tetB, tetC, tetL, tetZ, tetM, tetO, tetT, and tetX), class 1 integron-integrase gene (intI1) and bacterial communities were characterized using quantitative-PCR and Illumina MiSeq sequencing, in paddy soils exposed to inorganic fertilizer (NPK), animal-derived organic fertilizer (AOF, composted swine and/or chicken manure), plant-derived organic fertilizer (POF, rapeseed cake and/or astragalus) and commercial organic fertilizer (COF, composted of animal manure mix with crop residues) applications. Compared with NPK, AOF applications significantly increased the relative abundance of TRGs, which was predominantly expressed in the increase of the relative abundance of tetC, tetM, tetO, tetT, and tetX, while POF and COF had no significant effect on the relative abundance of TRGs. Principal coordinate analysis revealed that AOF and POF significantly altered bacterial communities in paddy soils relative to NPK, while COF had no significant change of bacterial communities. Variation partitioning analysis indicated that soil physicochemical properties were the decisive factors for the changes of TRGs in organic paddy fields. Furthermore, redundancy analysis and the Mantel test showed that TRG profiles in AOF applied paddy soils were strongly influenced by electrical conductivity (EC). Total nitrogen (TN) and organic matter (OM) affected the distribution of TRGs in COF and POF applied paddy soils through a different mechanism. This study provides insights into the impacts of different types of organic fertilizer on the profiles of TRGs in paddy soils.
Collapse
Affiliation(s)
- Li Qing
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China
| | - Dai Qigen
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Hu Jian
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
| | - Wu Hongjun
- Yangzhou Supervision & Inspection Center for Agri-products, Yangzhou, 225101, China
| | - Chen Jingdu
- Yangzhou Municipal Bureau of Agriculture and Rural Affairs, Yangzhou, 225000, China
| |
Collapse
|
15
|
Biochar, Ochre, and Manure Maturation in an Acidic Technosol Helps Stabilize As and Pb in Soil and Allows Its Vegetation by Salix triandra. ENVIRONMENTS 2022. [DOI: 10.3390/environments9070087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Past mining extraction activities still have a negative impact in the present time, the resulting metal(loid) contaminated soils affecting both the environment and human health. Assisted phytostabilization technology, combining soil conditioner application to immobilize metal(loid)s and plant growth to reduce erosion and leaching risks, is a useful strategy in the restoration of metal(loid) contaminated lands. However, contaminants will respond differently to a particular amendment, having their own specific characteristics. Therefore, in multi-contaminated soils, soil conditioner combination has been suggested as a good strategy for metal(loid) immobilization. In the present study, in a mesocosm experiment, organic (biochar and manure) and inorganic (ochre) amendments were evaluated in single and combined applications for their effect on metal(loid) stabilization and Salix triandra growth improvement, in an arsenic and lead highly contaminated soil. Specifically, the effects of these amendments on soil properties, metal(loid) behavior, and plant growth were evaluated after they aged in the soil for 6 months. Results showed that all amendments, except biochar alone, could reduce soil acidity, with the best outcomes obtained with the three amendments combined. The combination of the three soil conditioners has also led to reducing soil lead availability. However, only ochre, alone or combined with the other soil fertilizers, was capable of immobilizing arsenic. Moreover, amendment application enhanced plant growth, without affecting arsenic accumulation. On the contrary, plants grown on all the amended soils, except plants grown on soil added with manure alone, showed higher lead concentration in leaves, which poses a risk of return of lead into the soil when leaves will shed in autumn. Considering that the best plant growth improvement, together with the lowest increase in lead aerial accumulation, was observed in manure-treated soil, the addition of manure seems to have potential in the restoration of arsenic and lead contaminated soil.
Collapse
|
16
|
González D, Robas M, Fernández V, Bárcena M, Probanza A, Jiménez PA. Comparative Metagenomic Study of Rhizospheric and Bulk Mercury-Contaminated Soils in the Mining District of Almadén. Front Microbiol 2022; 13:797444. [PMID: 35330761 PMCID: PMC8940170 DOI: 10.3389/fmicb.2022.797444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/17/2022] [Indexed: 12/22/2022] Open
Abstract
Soil contamination by heavy metals, particularly mercury (Hg), is a problem that can seriously affect the environment, animals, and human health. Hg has the capacity to biomagnify in the food chain. That fact can lead to pathologies, of those which affect the central nervous system being the most severe. It is convenient to know the biological environmental indicators that alert of the effects of Hg contamination as well as the biological mechanisms that can help in its remediation. To contribute to this knowledge, this study conducted comparative analysis by the use of Shotgun metagenomics of the microbial communities in rhizospheric soils and bulk soil of the mining region of Almadén (Ciudad Real, Spain), one of the most affected areas by Hg in the world The sequences obtained was analyzed with MetaPhlAn2 tool and SUPER-FOCUS. The most abundant taxa in the taxonomic analysis in bulk soil were those of Actinobateria and Alphaproteobacteria. On the contrary, in the rhizospheric soil microorganisms belonging to the phylum Proteobacteria were abundant, evidencing that roots have a selective effect on the rhizospheric communities. In order to analyze possible indicators of biological contamination, a functional potential analysis was performed. The results point to a co-selection of the mechanisms of resistance to Hg and the mechanisms of resistance to antibiotics or other toxic compounds in environments contaminated by Hg. Likewise, the finding of antibiotic resistance mechanisms typical of the human clinic, such as resistance to beta-lactams and glycopeptics (vancomycin), suggests that these environments can behave as reservoirs. The sequences involved in Hg resistance (operon mer and efflux pumps) have a similar abundance in both soil types. However, the response to abiotic stress (salinity, desiccation, and contaminants) is more prevalent in rhizospheric soil. Finally, sequences involved in nitrogen fixation and metabolism and plant growth promotion (PGP genes) were identified, with higher relative abundances in rhizospheric soils. These findings can be the starting point for the targeted search for microorganisms suitable for further use in bioremediation processes in Hg-contaminated environments.
Collapse
Affiliation(s)
- Daniel González
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Marina Robas
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Vanesa Fernández
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Marta Bárcena
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Agustín Probanza
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Pedro A Jiménez
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| |
Collapse
|
17
|
Jauregi L, Epelde L, González A, Lavín JL, Garbisu C. Reduction of the resistome risk from cow slurry and manure microbiomes to soil and vegetable microbiomes. Environ Microbiol 2021; 23:7643-7660. [PMID: 34792274 DOI: 10.1111/1462-2920.15842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/04/2021] [Indexed: 11/30/2022]
Abstract
In cow farms, the interaction between animal and environmental microbiomes creates hotspots for antibiotic resistance dissemination. A shotgun metagenomic approach was used to survey the resistome risk in five dairy cow farms. To this purpose, 10 environmental compartments were sampled: 3 of them linked to productive cows (fresh slurry, stored slurry, slurry-amended pasture soil); 6 of them to non-productive heifers and dry cows (faeces, fresh manure, aged manure, aged manure-amended orchard soil, vegetables-lettuces and grazed soil); and, finally, unamended control soil. The resistome risk was assessed using MetaCompare, a computational pipeline which scores the resistome risk according to possible links between antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and human pathogens. The resistome risk decreased from slurry and manure microbiomes to soil and vegetable microbiomes. In total (sum of all the compartments), 18,157 ARGs were detected: 24% related to ansamycins, 21% to multidrugs, 14% to aminoglycosides, 12% to tetracyclines, 9% to β-lactams, and 9% to macrolide-lincosamide-streptogramin B. All but two of the MGE-associated ARGs were only found in the animal dejections (not in soil or vegetable samples). Several ARGs with potential as resistome risk markers (based on their presence in hubs of co-occurrence networks and high dissemination potential) were identified. As a precautionary principle, improved management of livestock dejections is necessary to minimize the risk of antibiotic resistance.
Collapse
Affiliation(s)
- Leire Jauregi
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
| | - Lur Epelde
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
| | - Aitor González
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
| | - José Luis Lavín
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
| | - Carlos Garbisu
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
| |
Collapse
|