Sustainable agriculture reviews. 49, Mitigation of antimicrobial resistance. Vol 2, Natural and synthetic approaches

"Sustainability rests on the principle that we must meet the needs of the present without compromising the ability of future generations to meet their own needs. Starving people in poor nations, obesity in rich nations, increasing food prices, on-going climate changes, increasing fuel and transportation costs, flaws of the global market, worldwide pesticide pollution, pest adaptation and resistance, loss of soil fertility and organic carbon, soil erosion, decreasing biodiversity, desertification, and so on. Despite unprecedented advances in sciences allowing to visit planets and disclose subatomic particles, serious terrestrial issues about food show clearly that conventional agriculture is not suited any longer to feed humans and to preserve ecosystems. Sustainable agriculture is an alternative for solving fundamental and applied issues related to food production in an ecological way. While conventional agriculture is driven almost solely by productivity and profit, sustainable agriculture integrates biological, chemical, physical, ecological, economic and social sciences in a comprehensive way to develop new farming practices that are safe and do not degrade our environment. In that respect, sustainable agriculture is not a classical and narrow science. Instead of solving problems using the classical painkiller approach that treats only negative impacts, sustainable agriculture treats problem sources. As most actual society issues are now intertwined, global, and fast-developing, sustainable agriculture will bring solutions to build a safer world. This book gathers review articles that analyze current agricultural issues and knowledge, then propose alternative solutions. It will therefore help all scientists, decision-makers, professors, farmers and politicians who wish to build a safe agriculture, energy and food system for future generations"--Back cover Preface Contents About the Editors Contributors Chapter 1: Strategies for Prevention and Containment of Antimicrobial Resistance 1.1 Introduction 1.2 Risk Factors for the Development of Antibacterial Drug Resistance 1.3 Ways of the Spread of Antibiotic Resistance 1.4 Major Mechanisms of Development of Antibacterial Drug Resistance 1.5 Strategies for Prevention of Antibacterial Drug Resistance and Reduction of Selective Pressure 1.5.1 Reduction of Selective Pressure 1.5.2 Diagnostic and Infection Prevention Stewardship 1.6 Strategies for Containment of Widespread Infection with Antibacterial Drug Resistant Bacteria 1.6.1 Infection Prevention Stewardship 1.6.2 Antibiotic Stewardship 1.6.3 Research and Development of New Antibacterial Drugs 1.7 Conclusion References Chapter 2: Dietary Management by Probiotics, Prebiotics and Synbiotics for the Prevention of Antimicrobial Resistance 2.1 Introduction 2.2 Dietary Management to Mitigate Antimicrobial Resistance 2.3 How Probiotics Reduce the Risk of Antimicrobila Resistance 2.3.1 Establishment of Intestinal Homeostasis 2.3.2 Modulation of Innate and Adaptive Immune System of Host 2.3.3 Antimicrobial Activity Against Pathogens 2.3.4 Interference with Colonization and Invasion of Pathogens 2.3.5 Modulation of Intestinal Barrier Function 2.4 How Prebiotics and Synbiotics Reduce the Risk of Antimicrobial Resistance 2.5 Synbiotic Mechanism of Action 2.6 Antimicrobial Resistance in Probiotics: An Important Aspect to Be Considered 2.7 Conclusion References Chapter 3: Plant Natural Products for Mitigation of Antibiotic Resistance 3.1 Introduction 3.2 Flavonoids 3.3 Phenolic Acids 3.4 Peptides 3.5 Essential Oils 3.6 Honey 3.7 Conclusion References Chapter 4: Essential Oils as Potential Antimicrobial Agents 4.1 Introduction 4.2 Overview of Antimicrobial Resistance 4.2.1 Mechanisms of Antimicrobial Resistance 4.2.2 Intrinsic Resistance 4.2.2.1 Restriction of Outer Membrane Permeability and the Efflux System 4.2.2.2 Antibiotic Inactivating Enzymes 4.2.3 Acquired Resistance 4.2.3.1 Horizontal Gene Transfer 4.2.3.2 Resistance by Gene Mutation 4.2.4 Adaptive Resistance 4.3 Strategies to Counteract Antimicrobial Resistance 4.3.1 Combination Drug Therapy 4.3.2 Bacteriophage Therapy 4.3.3 Use of Nanoparticles 4.4 Chemistry of Essential Oils 4.5 Essential Oils as Combination Therapy 4.6 Studies of Genomic and Proteomic of Microorganisms Treated with Essential Oils 4.6.1 Effects of Essential Oils on Genome Expression 4.6.2 Effects of Essential Oils on Proteomic Expression 4.7 Conclusion and Future Prospects References Chapter 5: Polymeric Antimicrobials with Quaternary Ammonium Moieties 5.1 Introduction 5.2 Polymeric Antimicrobials with Quaternary Ammonium Moieties 5.3 Antimicrobials Based on Natural Polymers 5.3.1 Cellulose Type Antimicrobials 5.3.2 Chitosan Type Antimicrobials 5.3.3 Dextran Type Antimicrobials 5.3.4 Pullulan Type Antimicrobials 5.3.5 Starch Type Antimicrobials 5.3.6 Cashew Gum Type Antimicrobials 5.3.7 Poly(lactide) Type Antimicrobials 5.4 Antimicrobials Based on Synthetic Polymers 5.4.1 Poly(amidoamine) Type Antimicrobials 5.4.2 Poly(urethane) Type Antimicrobials 5.4.3 Poly(siloxane) Type Antimicrobials 5.4.4 Poly(methacrylate) Type Antimicrobials 5.4.5 Poly(ethylene) Type Antimicrobials 5.5 Target Microorganisms Affected by Polymeric Antimicrobials Containing Quaternary Ammonium Moieties 5.6 Factors That Influence Antimicrobial Activity 5.7 Conclusions References Chapter 6: Nanoparticles: Powerful Tool to Mitigate Antibiotic Resistance 6.1 Introduction 6.1.1 Mechanisms of Antibiotic Resistance 6.1.1.1 Drug Inactivation or Alteration 6.1.1.2 Modification of Drug Binding Sites 6.1.1.3 Reduced Permeability of Antibiotics by Outer Membrane Proteins 6.1.1.4 Active Efflux Pumps Extruding Antibiotics 6.1.2 Current Status of Antibiotic Resistance 6.2 Nanoparticles: Boon in Post-antibiotic Era 6.2.1 Characterization of Nanoparticles 6.2.2 Classification of Nanoparticles 6.2.3 Synthesis of Nanoparticles 6.2.4 Inorganic Nanoparticles 6.2.4.1 Silver Nanoparticles 6.2.4.2 Gold Nanoparticles 6.2.4.3 Zinc Nanoparticles 6.2.4.4 Aluminium Nanoparticles 6.2.4.5 Copper Nanoparticles 6.2.4.6 Bismuth Nanoparticles 6.2.4.7 Titanium Nanoparticles 6.2.4.8 Magnesium Nanoparticles 6.2.4.9 Iron Containing Nanoparticles 6.2.4.10 Bimetallic Nanoparticles 6.2.5 Mechanism of Action of Metallic Nanoparticles 6.2.5.1 Generation of Reactive Oxygen Species 6.2.5.2 Release of Heavy Metal Ions 6.2.5.3 Affecting Bacterial Membrane Permeability 6.2.5.4 Adsorption of Nanoparticles to Bacterial Cell and Its Penetration 6.2.5.5 Affecting Nucleic Acid Replication 6.2.5.6 Disruption of Bacterial Biofilms 6.2.5.7 Efflux Inhibitory Properties of Nanoparticles 6.2.6 Antimicrobial Efficacy of Carbon Nanoparticles 6.2.6.1 Fullerenes 6.2.6.2 Carbon Nanotubes 6.2.6.3 Graphene 6.2.7 Organic Nanomaterials and Their Biomedical Applications 6.2.7.1 Improving the Bioavailability of Drug Molecules 6.2.7.2 Enhancing the Efficacy of Existing Metal Nanoparticles 6.2.7.3 Re-introducing Toxic Antimicrobials into Therapeutic Use 6.3 Potential Limitations of Metallic Nanoparticles 6.4 Future Research Directions 6.5 Conclusion References Chapter 7: Antimicrobial Peptides and Peptidomimetics for the Control of Antimicrobial Resistance 7.1 Introduction 7.1.1 Antimicrobial Peptides 7.1.2 Antimicrobial Peptides as Clinical Agents 7.1.3 Antimicrobial Peptide Classification 7.2 Mechanisms of Action 7.2.1 Membrane Lytic Antimicrobial Peptides 7.2.2 Intracellular Targets 7.2.3 Non-killing Actions 7.3 Key Physicochemical Properties 7.3.1 Length 7.3.2 Amino Acid Sequence 7.3.3 Charge 7.3.4 Hydrophobicity 7.3.5 Amphipathicity 7.3.6 Interplay Between the Physicochemical Properties of Antimicrobial Peptides and Peptidomimetics 7.4 Limitations and Challenges 7.4.1 Solubility and Proteolytic Degradation 7.4.2 Toxicity 7.4.3 Difficulty of Production and Manufacturing Cost 7.4.4 Resistance to Antimicrobial Peptides 7.5 Chemical Modifications and Peptidomimetics 7.5.1 Peptide Truncation and Antimicrobial Fragment Prediction 7.5.2 Unnatural Amino Acids and Side Chain Modifications 7.5.3 Covalent and Backbone Modifications 7.5.4 Chimeric Antimicrobial Peptides and Peptidomimetics 7.6 Concluding Remarks References Chapter 8: Exploiting the Achilles’ Heel of Iron Dependence in Antibiotic Resistant Bacteria with New Antimicrobial Iron Withdrawal Agents 8.1 Introduction 8.2 Iron Is Essential for Pathogenic Microorganisms 8.2.1 Microbial Iron Acquisition Virulence mechanisms 8.2.1.1 Iron Acquisition by Siderophore Systems 8.2.1.2 Heme Acquisition and Utilization 8.2.1.3 Transferrin, Lactoferrin and Ferritin 8.2.1.4 Fungal Iron Acquisition 8.2.2 Irreplaceable Iron Need Is an Achilles’ Heel of Microbes 8.3 Role of Iron in Host Defenses to Microbial Infection 8.3.1 Innate Iron Sequestration Immunity 8.3.2 Hypoferremic Response to Infection 8.3.3 Iron Dysregulation in Sepsis 8.3.4 Reactive Oxygen Species (ROS) Related Defense Mechanisms 8.4 Exploiting Microbial Iron Needs 8.4.1 Gallium a Non-functional Iron Mimic 8.4.2 Trojan Horse Antibiotic-Siderophore Conjugates 8.4.3 Synthetic Chelators to Intercept and Deny Iron 8.4.4 Hematologically Useful Iron Chelators Are Often Utilizable by Microbes 8.4.5 Problem of Weak Antimicrobial Activity of Low Molecular Weight Chelators 8.4.6 Requirements of New Microbial Specific Iron Withdrawal Agents 8.5 Novel Purpose Designed Antimicrobial Iron Sequestering Agents 8.5.1 Hydroxypyridinone, a Preferred Iron Ligand 8.5.2 Polymeric Iron Chelators 8.5.3 Low Host Toxicity 8.6 Antibiotic Resistance and Microbial Iron Needs 8.6.1 Resistance Mechanisms 8.6.2 Antibiotic Resistance Is Separate to Microbial Iron Needs 8.6.3 Antibiotic Resistance, Persisters, Bacterial Stress Response and Implications for Iron Withdrawal 8.7 Iron Withdrawal Is Effective for Antibiotic Resistant Microbes 8.7.1 Iron Chelators Inhibit Both Antibiotic Sensitive and Resistant Microbial Pathogens 8.7.2 Iron Chelators Suppress Infection from Antibiotic Resistant Microbes 8.7.3 Antimicrobial Iron Chelators Do Not Impede But Can Enhance Antibiotic Activities 8.8 Prospects and Future Directions 8.8.1 Prophylactics for Human Infection 8.8.2 Adjuncts with Antibiotics 8.8.3 Suppression of Antibiotic Resistance Formation and Transfer 8.8.4 Sepsis Therapy 8.9 Conclusions 8.10 Dedication References Chapter 9: Phage Biotechnology to Mitigate Antimicrobial Resistance in Agriculture 9.1 Introduction 9.2 Application of phages in Agriculture 9.2.1 Poultry 9.2.2 Pigs 9.2.3 Dairy Cows and Beef Cattle 9.2.3.1 Mastitis 9.2.3.2 Other Human and Bovine Pathogens 9.2.4 Horticulture 9.3 Conclusions References Chapter 10: The Role of Vaccines in Combating Antimicrobial Resistance 10.1 Introduction 10.2 Antimicrobial Resistance Is an Urgent Public Health Threat 10.3 Vaccines Are an Important Underutilized Tool to Help Address the Antimicrobial Resistance Problem 10.4 Vaccines Have Reduced Incidence and Evolution of Antimicrobial Resistant Bacterial Pathogens 10.4.1 Vaccines Reduce Circulating Antibiotic Resistant Strains and Antibiotic Use 10.4.1.1 Haemophilus influenzae Type b Vaccine 10.4.1.2 Pneumococcal Conjugate Vaccines 10.4.1.3 Typhoid Conjugate Vaccine 10.4.2 Vaccines Mediate Herd Immunity 10.4.3 Preventing Antimicrobial Resistance Using Viral Vaccines 10.4.3.1 Influenza Virus Vaccine 10.4.3.2 Rotavirus Vaccine 10.5 Vaccines Under Development with Potential to Reduce Antimicrobial Resistance 10.5.1 Bacterial Vaccines in Late-Stage Clinical Development 10.5.1.1 Clostridioides difficile Vaccines 10.5.1.2 Streptococcus pneumoniae Vaccines 10.5.1.3 Group B streptococcus Vaccines 10.5.2 Bacterial Vaccines in Early Stage Clinical or Pre-clinical Development 10.5.2.1 Enterobacteriaceae Vaccines 10.5.2.2 Other Gram Negative Bacterial Vaccines 10.5.2.3 Mycobacterium tuberculosis Vaccines 10.5.2.4 Shigella Vaccines 10.5.2.5 Non-typhoidal and Paratyphoid Salmonella Vaccines 10.5.2.6 Staphylococcus aureus Vaccines 10.5.3 Viral Vaccines Under Development 10.5.3.1 Respiratory Syncytial Virus Vaccines 10.5.3.2 Next Generation Influenza Vaccines 10.5.3.3 Human Immunodeficiency Virus Vaccines 10.6 Global Mobilization Utilizing Vaccines Against Antimicrobial Resistance 10.7 Challenges and Future Prospects 10.7.1 Barriers to Maximizing Licensed Vaccine Use 10.7.2 Efforts Towards Better Utilization of Vaccines to Optimize Their Impact on Antimicrobial Resistance and Future Prospects References Index I. Climate change. Soils and sustainable agriculture: a review; Soils and food sufficiency: a review / Rattan Lal Denitrification at sub-zero temperatures in arable soils: a review / Rebecca L. Phillips Re-thinking the conservation of carbon, water and soil: a different perspective / Thomas Francis Shaxson Cropping systems, carbon sequestration and erosion in Brazil: a review / Martial Bernoux,...[et al.] Influence of land use on carbon sequestration and erosion in Mexico: a review / J.D. Etchevers,...[et al.] Rhizodeposition of organic C by plant: mechanisms and controls / Christophe Nguyen Environmental costs and benefits of transportation biofuel production from food- and lignocellulose-based energy crops: a review / Enrico Ceotto Plant drought stress: effects, mechanisms and management / M. Farooq,...[et al.] II. Genetically modified organisms. Pharmaceutical crops in California, benefits and risks: a review / Michelle Marvier Coexistence of genetically modified and non-GM crops in the European Union: a review / Yann Devos,...[et al.] Agro-environmental effects due to altered cultivation practices with genetically modified herbicide-tolerant oilseed rape and implications for monitoring: a review / F. Graef Bacillus thuringiensis: applications in agriculture and insect resistance management: a review / Vincent Sanchis and Denis Bourguet Genetically modified glyphosate-tolerant soybean in the USA: adoption factors, impacts and prospects: a review / Sylvie Bonny III. Biodiversity. Small eats big: ecology and diversity of Bdellovibrio and like organisms, and their dynamics in predator-prey interactions / Shemesh Yair,...[et al.] Identification of traits implicated in the Rhizosphere competence of fluorescent pseudomonads: description of a strategy based on population and model strain studies / Xavier Latour,...[et al.] Progress in mechanisms of mutual effects between plants and the environment / Hong-Bo Shao, Li-Ye Chu, and Biao Li Biodiversity: function and assessment in agricultural areas: a review / Boris Clergue,...[et al.] Mixing plant species in cropping systems: concepts, tools and models: a review / E. Malézieux,...[et al.] Saffron, an alternative crop for sustainable agricultural systems, a review / F. Gresta,...[et al.] Digital imaging information technology applied to seed germination testing: a review / Antonio Dell' Aquila IV. Alternative control. Managing weeds with a dualistic approach of prevention and control: a review / Randy L. Anderson Mechanical destruction of weeds: a review / D. Chicouene Sustainable pest management for cotton production: a review / Jean-Philippe Deguine, Pierre Ferron, and Derek Russell Role of nutrients in controlling plant diseases in sustainable agriculture: a review / Christos Dordas Crop protection, biological control, habitat management and integrated farming / Pierre Ferron and Jean-Philippe Deguine Using grassed strips to limit pesticide transfer to surface water: a review / Jean-Guillaume Lacas,...[et al.] V. Alternative fertilisation. Recycling biosolids and lake-dredged materials to pasture-based animal agriculture: alternative nutrient sources for forage productivity and sustainability: a review / Gilbert C. Sigua Symbiotic nitrogen fixation in legume nodules: process and signaling: a review / Neera Garg and Geetanjali Factors responsible for nitrate accumulation: a review / Anjana,Shahid Umar, and Muhammad Iqbal Role of phosphate solubilizing microorganisms in sustainable agriculture, a review / Mohammad Saghir Khan, Almas Zaidi, and Parvaze A. Wani Iron and zinc biofortification strategies in dicot plants by intercropping with gramineous species; a review / Y. Zuo and F. Zhang Soil exploration and resource acquisition by plant roots: an architectural and modeling point of view / Claude Doussan Loïc Pagès, and Alain Pierret Methods for studying root colonization by introduced beneficial bacteria / Elisa Gamalero,...[et al.] VI. New farming systems. Sustainable urban agriculture in developing countries; a review / Hubert de Bon, Laurent Parrot, and Paule Moustier Nitrogen, sustainable agriculture and food security: a review / J.H.J. Spiertz Conversion to organic farming: a multidimensional research object at the crossroads of agricultural and social sciences: a review / Stéphane Bellon and Claire Lamine Triggering transitions towards sustainable development of the Dutch agricultural sector: transforum's approach / A. Veldkamp,...[et al.] Spatialising crop models / Robert Faivre,...[et al.] Iterative design and evaluation of rule-based cropping systems: methodology and case studies, a review / Philippe Debaeke,...[et al.] Agri-environmental indicators t assess cropping and farming systems: a review / Christian Bockstaller,...[et al.] Methodological progress in on-farm regional agronomic diagnosis: a review / Thierry Doré,...[et al.] Ex ante assessment of the sustainability of alternative cropping systems: implications for using multi-criteria decisions-aid methods, a review / Walid Sadok,...[et al.] Comparison of methods to assess the sustainability of agricultural systems: a review / Christian Bockstaller,...[et al.] Soil-erosion and runoff prevention by plant covers: a review / Víctor Hugo Durán Zuazo and Carmen Rocío Rodríguez Pleguezuelo Integration of soil structure variations with time and space into models for crop management: a review / J. Roger-Estrade,...[et al.] Management of grazing systems: from decision and biophysical models to principles for action / Michel Duru and Bernard Hubert VII. Pollutants in agrosystems. Cadmium in soils and cereal grains after sewage-sludge application on French soils: a review / Denis Baize Mobility, turnover and storage of pollutants in soils, sediments and waters: achievements and results of the EU project AquaTerra, a review / J.A.C. Barth,...[et al.] / Effect of metal toxicity on plant growth and metabolism: I. Zinc / Gyana Ranjan Rout and Premananda Das Phytoremediation of organic pollutants using mycorrhizal plants: a new aspect of rhizosphere interactions / Erik Jautris Joner and Corinne Leyval.

Sustainability rests on the principle that we must meet the needs of the present without compromising the ability of future generations to meet their own needs. Starving people in poor nations, obesity in rich nations, increasing food prices, on-going climate changes, increasing fuel and transportation costs, flaws of the global market, worldwide pesticide pollution, pest adaptation and resistance, loss of soil fertility and organic carbon, soil erosion, decreasing biodiversity, desertification, and so on. Despite unprecedented advances in sciences allowing to visit planets and disclose subatomic particles, serious terrestrial issues about food show clearly that conventional agriculture is not suited any longer to feed humans and to preserve ecosystems. Sustainable agriculture is an alternative for solving fundamental and applied issues related to food production in an ecological way. While conventional agriculture is driven almost solely by productivity and profit, sustainable agriculture integrates biological, chemical, physical, ecological, economic and social sciences in a comprehensive way to develop new farming practices that are safe and do not degrade our environment. In that respect, sustainable agriculture is not a classical and narrow science. Instead of solving problems using the classical painkiller approach that treats only negative impacts, sustainable agriculture treats problem sources. As most actual society issues are now intertwined, global, and fast-developing, sustainable agriculture will bring solutions to build a safer world.

This book gathers review articles that analyze current agricultural issues and knowledge, then propose alternative solutions. It will therefore help all scientists, decision-makers, professors, farmers and politicians who wish to build a safe agriculture, energy and food system for future generations.

Antibiotics have drastically improved the health and life expectancy of humans, yet the abrupt increase of antibiotic usage for animals, agriculture and healthcare has induced antimicrobial resistance. Antimicrobial resistance is leading to resurgence of deadly infectious diseases, calling for new cures. This book presents advanced therapies based on new and complementary drugs, and alternative techniques and strategies, such as phages, probiotics, flavonoids, essential oils, cellulose, peptides, nano delivery, iron starvation and vaccines