Infectious Diseases and Pathology of Reptiles

Cover
Half Title
Title Page
Copyright Page
Dedication
Contents
2020 Preface, Volume 1
Acknowledgments
Editors
Contributors
1. Overview of Biology, Anatomy, and Histology of Reptiles
	1.1 General Concepts and Phylogenetic Relationships of the Reptilia
	1.2 Extant Taxonomic Orders of the Reptilia
		1.2.1 Testudines
		1.2.2 Crocodylia
		1.2.3 Rhynchocephalia
		1.2.4 Squamata
	1.3 Thermal Biology
	1.4 Reviews by System and Organs
		1.4.1 Integumentary System
		1.4.2 Musculoskeletal System
		1.4.3 Digestive System
		1.4.4 Respiratory System
		1.4.5 Urinary System
		1.4.6 Reproductive System
		1.4.7 Cardiovascular System
		1.4.8 Lymphatic System
		1.4.9 Hemopoietic System
		1.4.10 Endocrine Organs
		1.4.11 Nervous System
		1.4.12 Eye
		1.4.13 Ear
		1.4.14 Vomeronasal Organ
		1.4.15 Salt Glands
		1.4.16 Infrared Detection Organs
	Acknowledgments
	References
2. Immunology of Reptiles
	2.1 General Concepts
	2.2 Innate Defense Mechanisms
		2.2.1 Surface Barriers
		2.2.2 Nonspecific Humoral Factors and Mediators of Inflammation
		2.2.3 Nonspecific Immune Cells and Associated Elements
	2.3 Specific Defense Mechanisms
		2.3.1 Lymphocytes
		2.3.2 Lymphoid Organs
		2.3.3 Immunoglobulins (Antibodies)
		2.3.4 Antibody Response to Antigens
		2.3.5 Cell-Mediated Immune Responses
		2.3.6 Memory
		2.3.7 Factors Affecting the Immune Response
		2.3.8 The Immune Response during Bacterial Diseases
		2.3.9 The Immune Response during Viral Diseases
		2.3.10 The Immune Response during Parasitic Diseases
		2.3.11 Vaccination
		2.3.12 Future
	References
3. Hematology of Reptiles with a Focus on Circulating Inflammatory Cells
	3.1 General Concepts of Hematology
	3.2 Collection and Handling of Blood Samples
		3.2.1 Chelonia
		3.2.2 Crocodylia
		3.2.3 Sauria
		3.2.4 Ophidia
		3.2.5 Serial Blood Sampling
	3.3 Hematology Procedures
		3.3.1 Erythrocytes
		3.3.2 Leukocytes
		3.3.3 Thrombocytes
		3.3.4 Total Protein and Fibrinogen
		3.3.5 Reference Intervals
	3.4 General Considerations
	3.5 Erythrocytes and Erythrocyte Responses in Disease
		3.5.1 Normal Erythrocyte Morphology and Function
		3.5.2 Abnormalities in Erythrocytes
		3.5.3 Anemia and Polycythemia
	3.6 Leukocytes and Leukocyte Responses in Disease
		3.6.1 Heterophils
		3.6.2 Eosinophils
		3.6.3 Basophils
		3.6.4 Lymphocytes
		3.6.5 Plasma Cells
		3.6.6 Monocytes
		3.6.7 Azurophils
		3.6.8 Tumors of Hematopoietic Tissue
	3.7 Thrombocytes and Thrombocyte Responses in Disease
	3.8 Infectious Agents in the Peripheral Blood
		3.8.1 Hemoparasites
		3.8.2 Viral Inclusions in Blood Cells
		3.8.3 Bacteria
	References
4. Reptile Necropsy Techniques
	4.1 Introduction
		4.1.1 Purpose of Necropsy
		4.1.2 Essential Components of a Necropsy and Interpretation of Findings
	4.2 Necropsy Preparations
		4.2.1 Costs Associated with a Necropsy
		4.2.2 Carcass Preservation and Shipping
		4.2.3 Facilities and Equipment
		4.2.4 Human Safety Precautions
		4.2.5 Preparation and Documentation
	4.3 Gross Examination
		4.3.1 Biological Measurements
		4.3.2 External Examination
		4.3.3 Dissection and Internal Examination
	4.4 Necropsy Sampling
		4.4.1 Cytology
		4.4.2 Light Microscopy (Histopathology)
		4.4.3 Electron Microscopy
		4.4.4 Toxicology
		4.4.5 Microbiology
		4.4.6 Molecular Diagnostic Tests
		4.4.7 Specific Pathogen Detection and Identification
	4.5 After the Necropsy
		4.5.1 Carcass Disposal and Disinfection Procedures
		4.5.2 Electronic Storage, Archiving, and Retrieval of Reports
		4.5.3 Archival Preservation of Tissues
	4.6 Conclusions
	Acknowledgments
	References
5. Host Response to Infectious Agents and Identification of Pathogens in Tissue Sections
	5.1 Introduction
	5.2 Reptilian Leukocytes and Macrophages
		5.2.1 Granulocytes
		5.2.2 Heterophils
		5.2.3 Eosinophils
		5.2.4 Basophils and Mast Cells
		5.2.5 Monocytes, Azurophils, and Macrophages
		5.2.6 Lymphocytes and Plasma Cells
	5.3 Distribution of Lymphoid and Hematopoietic Tissue
	5.4 The Inflammatory Response
		5.4.1 Gross Appearance of Exudates
		5.4.2 Time Course of Inflammatory Processes
		5.4.3 Temperature Effects on Inflammatory Responses
		5.4.4 Granuloma Formation
	5.5 Proliferative Host Responses
		5.5.1 Cryptosporidiosis
		5.5.2 Viral Diseases and Proliferative Lesions
		5.5.3 Other Examples of Proliferative Responses
	5.6 Lesions and Tissue Deposits Associated with Inflammation
		5.6.1 Tissue Responses Secondary to Inflammation
		5.6.2 Splendore-Hoeppli Reaction
		5.6.3 Amyloidosis
		5.6.4 Immune Complex–Associated Glomerulonephritis
	5.7 Detection of Infectious Agents in Tissue Sections
		5.7.1 Viral Infections
		5.7.2 Bacterial Infections
		5.7.3 Fungal Infections
		5.7.4 Parasites in Tissue Sections
	5.8 Immunohistochemistry and In Situ Hybridization
	References
6. Introduction to Basic Cytodiagnosis
	6.1 Introduction
	6.2 Aspects of Sample Collection, Handling, and Processing
	6.3 Principles of Cytological Evaluation
		6.3.1 Introduction
		6.3.2 General Cytological Categories
	6.4 Cytology of Commonly Sampled Organ Systems
		6.4.1 Cutaneous Lesions
		6.4.2 Coelomic Fluid
		6.4.3 Synovial Fluid
		6.4.4 Respiratory Tract
		6.4.5 Digestive Tract
		6.4.6 Urogenital Tract
		6.4.7 Cerebrospinal Fluid
	6.5 Additional Diagnostic Procedures Using Cytology Specimens
	References
7. Identifying Reptile Pathogens Using Electron Microscopy
	7.1 General Comments
	7.2 Historical Perspectives
	7.3 Electron Microscopy
		7.3.1 Positive Staining Transmission Electron Microscopy (PSEM)
		7.3.2 Negative Staining Transmission Electron Microscopy (NSEM)
		7.3.3 Scanning Electron Microscopy
	7.4 Collection of Samples
		7.4.1 Blood Cells and Cell Cultures
		7.4.2 Biopsies
		7.4.3 Postmortem Specimens
		7.4.4 Paraffin-Embedded Tissues
		7.4.5 Feces, Aspirates, and Washings for Negative Staining Electron Microscopy
	7.5 Identifying Pathogens in Cells and Tissues
		7.5.1 Understanding the Ultrastructure of Normal Cells
		7.5.2 Viruses
		7.5.3 Bacteria
		7.5.4 Parasites
		7.5.5 Fungi
	Acknowledgments
	References
8. Molecular Diagnostics
	8.1 General Comments
	8.2 Blotting Techniques
		8.2.1 General Considerations
		8.2.2 Southern Blotting
		8.2.3 Northern Blotting
		8.2.4 Western Blotting
	8.3 Two-Dimensional Polyacrylamide Gel Electrophoresis
		8.3.1 Introduction
		8.3.2 The Procedure
		8.3.3 Interpretation of Results, Pitfalls, and Limitations
		8.3.4 Advantages and Disadvantages
	8.4 Arrays
		8.4.1 Introduction
		8.4.2 Gene Expression Arrays
		8.4.3 Protein Arrays
		8.4.4 Tissue Arrays
	8.5. In Situ. Hybridization
		8.5.1 Introduction
		8.5.2 The Procedure
		8.5.3 Interpretation of Results, Pitfalls, and Limitations
	8.6 Polymerase Chain Reaction
		8.6.1 Introduction
		8.6.2 The Procedure
		8.6.3 Results
		8.6.4 Variations of PCR
		8.6.5 Reverse Transcription PCR
		8.6.6 Real-Time PCR
		8.6.7 Interpretation of Results
		8.6.8 Future Directions
	8.7 Molecular Phylogeny
		8.7.1 Introduction
		8.7.2 Molecular Evolution
		8.7.3 Sequence Selection
		8.7.4 Sequence Alignment
		8.7.5 Tree-Building Methods
		8.7.6 Methods of Measuring Confidence
		8.7.7. Further Reading
	8.8 Next Generation Sequencing
		8.8.1 Introduction
		8.8.2 NGS Technologies and Methods
		8.8.3 NGS Applications
		8.8.4 Limitations of NGS
	Acknowledgments
	References
9. Serodiagnostics
	9.1 General Comments
	9.2 Types of Serological Assays
		9.2.1 Serum Neutralization Test
		9.2.2 Hemagglutination and Hemagglutination Inhibition
		9.2.3 Enzyme-Linked  Immunosorbent Assay
		9.2.4 Immunofluorescence Test
		9.2.5 Immunoperoxidase
		9.2.6 Western Blot Assay
	9.3 Titer, Titrations, Quantitations, and Pitfalls
	9.4 Establishing Test Cutoffs
	9.5 Sensitivity, Specificity, Positive Predictive Values, and Negative Predictive Values
	9.6 Collection and Handling of Blood Samples
	9.7 Serology for Viral Exposure
		9.7.1 Adenoviruses
		9.7.2 Herpesviruses
		9.7.3 Iridoviruses
		9.7.4 Paramyxoviruses
		9.7.5 Reoviruses
		9.7.6 Arboviruses
		9.7.7 Boid Inclusion Body Disease
	9.8 Serology for Bacterial Exposure
		9.8.1 Mycoplasma
		9.8.2 Leptospira
		9.8.3 Coxiella
	9.9 Serology for Parasite Exposure
		9.9.1 Cryptosporidiosis
		9.9.2 Spirorchiidiasis
	9.10 Factors Affecting the Immune Response in Reptiles
	Acknowledgments
	References
10. Viruses and Viral Diseases of Reptiles
	10.1 General Comments
	10.2 Herpesviridae (Order Herpesvirales)
		10.2.1 General Characteristics and Taxonomy
		10.2.2 Testudines
		10.2.3 Crocodylia
		10.2.4 Squamata
	10.3. Adenoviridae
		10.3.1 General Characteristics and Taxonomy
		10.3.2 Testudines
		10.3.3 Crocodylia
		10.3.4 Squamata
		10.3.5 Squamata: Mixed Infections
		10.3.6 Isolation of Adenoviruses and Detection of Anti-Adenoviral Antibodies
	10.4 Poxviridae
		10.4.1 General Characteristics and Taxonomy
		10.4.2 Testudines
		10.4.3 Crocodylia
		10.4.4 Squamata
	10.5 Iridoviridae
		10.5.1 General Characteristics and Taxonomy
		10.5.2 Ranaviruses
		10.5.3 Hemocytiviruses (Erythrocytic Necrosis Viruses)
		10.5.4 Invertebrate Iridoviruses
	10.6 Papillomaviridae
		10.6.1 General Characteristics and Taxonomy
		10.6.2 Testudines
		10.6.3 Squamata
	10.7. Parvoviridae
		10.7.1 General Characteristics and Taxonomy
		10.7.2 Squamata
	10.8. Circoviridae
		10.8.1 General Characteristics and Taxonomy
		10.8.2 Testudines
		10.8.3 Squamata
	10.9 Anelloviridae
		10.9.1 General Characteristics and Taxonomy
		10.9.2 Testudines
	10.10 Retroviridae (Order Ortervirales)
		10.10.1 General Characteristics and Taxonomy
		10.10.2 Testudines
		10.10.3 Crocodylia
		10.10.4 Rhynchocephalia
		10.10.5 Squamata
	10.11 Riboviria
		10.11.1 Reoviridae
		10.11.2 Mononegavirales (Class Monjiviricetes, Subphylum .Haploviricotina., Phylum .Negarnaviricota., Realm .Riboviria.)
		10.11.3 Bunyavirales (Class Ellioviricetes, Subphylum .Polyploviricotina., Phylum .Negarnaviricota., Realm .Riboviria.)
		10.11.4 Togaviridae
		10.11.5 Flaviviridae
		10.11.6 Caliciviridae
		10.11.7 Picornaviridae. (Order .Picornavirales.)
		10.11.8 Nidovirales
		10.11.9 Deltavirus
	10.12 Miscellaneous Viruses
	10.13 Suspected Viral Diseases
		10.13.1 Squamata
	Acknowledgment
	References
11. Bacterial Diseases of Reptiles
	11.1 General Comments
	11.2 Bacteriology in Reptiles: Understanding What.’.s Normal
		11.2.1 The Gut Microbiome
		11.2.2 The Respiratory Tract Microbiome
		11.2.3 Microbial Communities in  Other Tissues
	11.3 Pseudomonas
	11.4 Aeromonas
	11.5 Salmonella
	11.6 Burkholderia
	11.7 Citrobacter
	11.8 Serratia
	11.9 Pasteurella
	11.10 Erysipelothrix
	11.11 Neisseria
	11.12 Elizabethkingia
	11.13 Vibrio
	11.14 Listeria
	11.15 Helicobacter
	11.16 Campylobacter
	11.17 Streptococcus
	11.18 Enterococcus
	11.19 Anaerobes
	11.20 Actinomycetales
		11.20.1 Mycobacterium
		11.20.2 Nocardia
		11.20.3 Dermatophilus and Austwickia
		11.20.4 Devriesea agamarum
	11.21 Mycoplasma
		11.21.1 Chelonia
		11.21.2 Crocodylia
		11.21.3 Sauria
		11.21.4 Ophidia
	11.22 Chlamydia
		11.22.1 Chelonia
		11.22.2 Crocodylia
		11.22.3 Sauria
		11.22.4 Ophidia
	11.23 Leptospira
	11.24 Borrelia
	11.25 Coxiella
	11.26 Ehrlichia
	11.27 Mixed and Miscellaneous Aerobic Bacterial Infections
		11.27.1 Spiral-Shaped Bacterium in a Rhinoceros Iguana
		11.27.2 Shell Disease of Aquatic Turtles
		11.27.3 Subcutaneous and Tissue Abscesses and Masses
		11.27.4 Bacterial Infections of the Eye and Orbit
		11.27.5 Stomatitis, Gingivitis, and Pharyngitis
		11.27.6 Pneumonia
		11.27.7 Bacteremia and Osteomyelitis
		11.27.8 Miscellaneous Bacterial Infections
	Acknowledgments
	References
12. Mycotic Diseases of Reptiles
	12.1 General Comments
	12.2 An Overview of the Fungi
	12.3 Normal Mycobiota of Reptiles
	12.4 Mycoses
		12.4.1 Dermatomycosis
		12.4.2 Systemic Mycosis
	12.5 Diagnostic Evaluation and Interpretation
	12.6 Agents of Mycosis
		12.6.1 Hyalohyphomycotic Agents
		12.6.2 Dematiaceous Fungi
		12.6.3 Yeast
		12.6.4 Dimorphic Fungi
		12.6.5 Microsporidians
	12.7 Conclusion
	References
13. Parasites and Parasitic Diseases of Reptiles
	13.1 General Comments
	13.2 Protozoans
		13.2.1 Amoebae
		13.2.2 Parabasalia and Euglenozoa
		13.2.3 Apicomplexa: Nonhemoparasitic
		13.2.4 Apicomplexa: Hemoparasitic
	13.3 Cestoda
		13.3.1 Pseudophyllidea
		13.3.2 Proteocephalidea
		13.3.3 Trypanorhyncha
		13.3.4 Cyclophyllidea
	13.4 Trematoda
		13.4.1 Ochetosomatidae and Plagiorchiidae
		13.4.2 Spirorchiidae
		13.4.3 Diplostomatidae
		13.4.4 Rhytidodidae
		13.4.5 Hemiuridae
	13.5 Nematoda
		13.5.1 Ascaridoidea
		13.5.2 Cosmocercoidea
		13.5.3 Diaphanocephaloidea
		13.5.4 Filarioidea
		13.5.5 Dracunculoidea
		13.5.6 Diplotriaenoidea
		13.5.7 Gnathostomatoidea
		13.5.8 Spiruroidea
		13.5.9 Physalopteroidea
		13.5.10 Dioctophymatoidea
		13.5.11 Rhabditoidea
		13.5.12 Oxyuroidea
		13.5.13 Trichinelloidea
		13.5.14 Camallanoidea
	13.6 Acanthocephala
		13.6.1 Testudines
		13.6.2 Squamata
	13.7 Pentastomida
		13.7.1 Testudines
		13.7.2 Crocodylia
		13.7.3 Squamata
	13.8 Annelida
		13.8.1 Hirudinea
	13.9 Crustacea
		13.9.1 Cirripedia
	13.10 Acari
		13.10.1 Parasitiformes
		13.10.2 Acariformes
	13.11 Diptera
		13.11.1 Testudines
		13.11.2 Squamata
	13.12 Siphonaptera
	Acknowledgments
	References
14. Isolation of Pathogens
	14.1 General Comments
	14.2 Sample Handling
		14.2.1 Sample Collection
		14.2.2 Sample Preservation and Shipping
		14.2.3 Sample Receipt
	14.3 Approach to Microorganism Isolation
		14.3.1 Viral Isolation
		14.3.2 Bacterial Isolation
		14.3.3 Fungal Isolation
	References
Index