Antimicrobial Research and One Health in Africa

Foreword
Preface
Contents
Chapter 1: Why Context Matters: Understanding Social and Behavioural Aspects of Antimicrobial Use and Resistance in Africa
	1.1 Introduction
	1.2 Policy Context
	1.3 Legal Context
	1.4 Biomedicine’s Power
	1.5 Self-Medication
	1.6 The Limits to State Health Services
	1.7 How Perceptions of Inequality and Access Influence Supply
	1.8 Conclusion
	References
Chapter 2: Antimicrobial Stewardship in Africa
	2.1 Antimicrobial Use and Resistance in Humans
	2.2 Antimicrobial Use and Resistance in Animals
	2.3 AMR in the Environment
	2.4 One Health Approach and AMR
	2.5 Antimicrobial Stewardship in Africa
	2.6 Recommendations
	2.7 Conclusion
	References
Chapter 3: Etiology of Early-Onset Bacterial Sepsis and Antibiotic Resistance in Neonates: A Case Study in an Algerian Neonatal Intensive Care Unit
	3.1 Introduction
	3.2 Methods
		3.2.1 Study Period and Inclusion Criteria
		3.2.2 Operational Definitions
		3.2.3 Data Collection and Analysis
	3.3 Results
		3.3.1 Demographic and Clinical Characteristics
		3.3.2 Profile of Pathogens
	3.4 Antimicrobial Susceptibility
	3.5 Predictors of Early-Onset Bacterial Sepsis
	3.6 Discussion
	References
Chapter 4: Genetics of Viral Resistance: Clinical Relevance and Role in Viral Disease Outbreak
	4.1 Introduction
	4.2 Origin and Mechanism of Viral Resistance
	4.3 Molecular Basis of Immune Evasion by Viruses
	4.4 Detection and Monitoring of Viral Resistance
		4.4.1 Laboratory Investigation
		4.4.2 Resistance Testing
	4.5 Clinical Implications of Viral Resistance
	4.6 Role of Viral Resistance in Disease Outbreak
	4.7 Innovative Approaches to Prevention and Elimination of Viral Resistance
	4.8 Conclusion
	References
Chapter 5: Distribution and Prevalence of Antimicrobial Resistance of NTS Salmonella Isolated from Farm Animals and Animal Food Products in Africa
	5.1 Background
	5.2 Introduction
	5.3 Salmonella Taxonomic Classification
	5.4 Morphology, Bacteriological Culture, and Isolation Procedures
		5.4.1 Collection, Transport, and Storage of Specimens for Salmonella Detection
		5.4.2 Salmonella Culture and Isolation
		5.4.3 Biochemical Identification
		5.4.4 Serological Identification for Salmonella
		5.4.5 Identification of Salmonella by MALDI-TOF MS
		5.4.6 Antimicrobial Susceptibility Testing for Salmonella
	5.5 Host Specificity and Adaptation
	5.6 Sources and Modes of Salmonella Transmission as Zoonosis Pathogen
	5.7 Manifestations of Salmonella Disease and Virulence Genes Involved
	5.8 Antimicrobial Resistance in NTS Serotypes
	5.9 Methods
	5.10 Results
		5.10.1 Literature Search
		5.10.2 NTS per African Regions
		5.10.3 Distribution of NTS by Origin and Serotypes
		5.10.4 Antibiotic Resistance Pattern of NTS in Different Sources
		5.10.5 Antibiotics Resistance Patterns in S. Enteritidis
		5.10.6 Antibiotics Resistance Patterns in S. Typhimurium
		5.10.7 Antibiotics Resistance Patterns in S. Kentucky
	5.11 Discussion
	5.12 Conclusion
	References
Chapter 6: The Current Status of Antibiotic-Resistant Bacteria and Resistance Genes in African Aquaculture
	6.1 Introduction
	6.2 The Sources of ARB and ARGs in Aquaculture
		6.2.1 Application of Antibiotics in Aquaculture
		6.2.2 Animal Manure and Integrated Aquaculture as ARB and ARGs Sources
		6.2.3 Aquatic Environment as a Source of ARB and ARGs
		6.2.4 Wastewater Treatment Plants as ARB and ARGs Sources
		6.2.5 Hospitals and Pharmaceutical Industries as ARB and ARGs Sources
		6.2.6 Aquaculture Workers as ARB and ARGs Sources
	6.3 Factors Causing ARB and ARGs in Aquaculture
		6.3.1 Antibiotics Overuse and Misuse
		6.3.2 Regulatory Barriers
		6.3.3 Availability, Accessibility and Affordability of Antibiotics
		6.3.4 Incorrect Antibiotic Prescriptions
		6.3.5 Prolonged Use of the Same Antibiotics
	6.4 Types of ARB and ARG in Aquaculture
	6.5 The Socioeconomic Consequences of ARB and ARGs in Aquaculture
		6.5.1 The Transfer of ARB and ARGs from Aquaculture to Humans
		6.5.2 Human Health Risk
		6.5.3 Economic Consequences
		6.5.4 Increased Human Deaths
	6.6 Conclusion
	6.7 Recommendations
	References
Chapter 7: Occurrence and Health Risks of Antibiotic Resistance in African Aquatic Systems
	7.1 Introduction
	7.2 Occurrence in Aquatic Systems
		7.2.1 Sources and Drivers
		7.2.2 Wastewater Systems
		7.2.3 Surface Aquatic Systems
		7.2.4 Rainwater Harvesting Systems
		7.2.5 Groundwater Systems
	7.3 Behavior, Dissemination, and Fate
		7.3.1 Hydrologically Driven Dissemination
		7.3.2 Horizontal Gene Transfer and the Role of Mobile Genetic Elements
			7.3.2.1 Conjugation
			7.3.2.2 Natural Transformation
			7.3.2.3 Transduction
		7.3.3 Fate of Antibiotic Resistance in Aquatic Systems
	7.4 Human Health Risks, Mitigation, and Policy Perspectives
	7.5 Removal of Antibiotic Resistance in Aquatic Systems
	7.6 Future Perspectives and Research Directions
		7.6.1 Knowledge Gaps
		7.6.2 Challenges and Proposed Solutions
			7.6.2.1 Lack of Accredited and Well-Equipped Analytical Laboratories
			7.6.2.2 Lack of Research Funding
			7.6.2.3 Lack of Research and Technical Expertise
	7.7 Conclusions
	References
Chapter 8: The Current State of Antimicrobial Use in Bovine Mastitis in Various African Countries
	8.1 Introduction
	8.2 Associated Causative Agents (Mastitis and Contributory Microbes)
	8.3 Diagnosis and Treatment
	8.4 Antimicrobial Resistance
	8.5 Occurrence of Mastitis in African Regions
	8.6 Antimicrobial Resistance and Mastitis in Africa
	8.7 Prevention and Control
	8.8 Conclusion
	References
Chapter 9: Microbiological Safety and Antimicrobial Resistance in Fresh Produce Production in Africa
	9.1 Introduction
	9.2 Microorganisms of Public Health Significance in Fresh Produce in Africa
	9.3 Antimicrobial Resistance (AMR) in Fresh Produce in Africa
	9.4 Sources of Antimicrobial-Resistant Pathogen Contamination
		9.4.1 On-Farm Sources of Contamination
			9.4.1.1 Soil
			9.4.1.2 Seeds
			9.4.1.3 Organic Manure/Soil Amendment
		9.4.2 Exposure to Contaminated Water
			9.4.2.1 Irrigation
			9.4.2.2 Sewage Sludge/Runoff Water
		9.4.3 Faecal Contamination from Livestock and Wild Animals
			9.4.3.1 Farm Workers
			9.4.3.2 Farm Implements
	9.5 Processing/Postharvest Sources of Contamination
		9.5.1 Washing
		9.5.2 Handling During Processing
		9.5.3 Transport, Distribution, and Storage Equipment
		9.5.4 Handling During Retail
		9.5.5 Cross-Contamination During Food Preparation
	9.6 Strategies for Controlling Antimicrobial-Resistant Pathogens in Fresh Produce
	References
Chapter 10: Biosecurity and Disinfectant Resistance in a Post-antibiotic Era
	10.1 Introduction
	10.2 Alternatives to Antibiotics
		10.2.1 Vaccines
		10.2.2 Bacteriophages
	10.3 Biosecurity in Animal Production
		10.3.1 Bovine Mastitis
		10.3.2 Poultry
	10.4 Swine
	10.5 Biosecurity in Human Health
	10.6 Development of Disinfectant Resistance
	10.7 Metabolic Changes in the Presence of Disinfectants
	10.8 Methods to Discover Novel Disinfectant Resistance Mechanisms
	10.9 Disinfectant Resistance Going Forward
	10.10 Conclusion
	References
Chapter 11: The Linkage Between Antibiotic and Disinfectant Resistance
	11.1 Introduction
	11.2 The Link Between Antibiotic and Disinfectant Resistance
	11.3 The State of Antibiotic Resistance
	11.4 Development of Antibiotic Resistance
	11.5 Dissemination of Antibiotic Resistance
		11.5.1 Dissemination of Antibiotic Resistance in Wild Animals
		11.5.2 Dissemination of Antibiotic Resistance in Agriculture
		11.5.3 Dissemination of Antibiotic Resistance in African Communities
	11.6 Disinfectants as Antimicrobial Agents
		11.6.1 Disinfectant Use in Africa
	11.7 The Relationship Between Antibiotic and Disinfectant Susceptibility
		11.7.1 Potential Co-selective Nature of Disinfectants and Antibiotics
		11.7.2 Resistance Repertoires and Resistance Mechanisms
		11.7.3 The Link Between Disinfectant and Antibiotic Susceptibilities
	11.8 Resistance Acquisition and Transfer
		11.8.1 Cross-Resistance to Antibiotics
		11.8.2 Plasmid Maintenance
		11.8.3 Inactivation and Degradation
		11.8.4 Cell Surface Alterations and Decreased Compound Uptake
		11.8.5 Efflux
	11.9 Efflux Pumps as Joint Resistance Mechanisms
		11.9.1 Classification of Efflux Pumps
		11.9.2 Regulation of Efflux Pumps
		11.9.3 Activity of Efflux Pumps
			11.9.3.1 Qac Proteins Involved in Efflux
			11.9.3.2 RND Efflux Systems
		11.9.4 Efflux Pump Adaptations
			11.9.4.1 Constitutive and Transient Expression
	11.10 Concluding Remarks
	References
Chapter 12: The Use of Nanomaterials for the Elimination of Antibiotic-Resistant Bacteria from Water and Wastewater: An African Overview
	12.1 Introduction
	12.2 Antibiotic Resistance Mechanisms in Bacteria
	12.3 Antimicrobial Resistance Transmission in the Environment
	12.4 Antibiotic-Resistant Bacteria (ARB) and Antibiotic Resistance Genes (ARGs) in African Water
		12.4.1 Wastewater
		12.4.2 River Water
		12.4.3 Drinking Water
	12.5 Current Treatment Technologies of Water/Wastewater
		12.5.1 The Application of NPs for ARB and ARGs
		12.5.2 NPs-Microbes Interactions and Antimicrobial Mechanism
	12.6 Some African Studies on the Use of NPs for Water and Wastewater Treatment
	12.7 Conclusion
	References
Chapter 13: Biocidal Activity of Plant Extracts: The Case of Algeria
	13.1 Introduction
	13.2 The Biocidal Activity of Algerian Plants
		13.2.1 Asteraceae
		13.2.2 Anacardiaceae
		13.2.3 Apiaceae
		13.2.4 Chenopodiaceae
		13.2.5 Fabaceae
		13.2.6 Lamiaceae
		13.2.7 Lauraceae
		13.2.8 Myrtaceae
		13.2.9 Pinaceae
		13.2.10 Rutaceae
	13.3 Conclusion
	References
Chapter 14: The Combined Use of African Natural Products and Conventional Antimicrobials: An Alternative Tool Against Antimicrobial Resistance
	14.1 Introduction
		14.1.1 Natural Product Classification
		14.1.2 Global Natural Product Use and Traditional Health Systems
		14.1.3 Natural Product Use in the African Healthcare System
		14.1.4 Natural Products with Antimicrobial Properties
	14.2 Exploring the Combination of Natural Products with Conventional Antimicrobial Agents to Address Antimicrobial Resistance (AMR)
		14.2.1 Interactive Antimicrobial Profiling of Combinations
			14.2.1.1 Synergistic Interactions
			14.2.1.2 Antagonistic Interactions
			14.2.1.3 Additive and Non-interactive Interactions
		14.2.2 Conventional Antimicrobials in Synergistic Combinations with Essential Oils
		14.2.3 Conventional Antimicrobials in Synergistic Combinations with Plant Extracts
		14.2.4 Conventional Antimicrobials in Synergistic Combinations with Culinary Herbs, Spices and Other Plant-Based Foods
		14.2.5 Conventional Antimicrobials in Synergistic Combinations with Herbal Teas
		14.2.6 Conventional Antimicrobials in Synergistic Combinations with Bee Products
	14.3 Conventional Antimicrobials in Antagonistic Interactions with Natural Products
	14.4 Discussion and Conclusion
	References
Index