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Microbiology

D | Taxonomy of Clinically Relevant Microorganisms

Microbiology D | Taxonomy of Clinically Relevant Microorganisms
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  1. Preface
  2. 1 An Invisible World
    1. Introduction
    2. 1.1 What Our Ancestors Knew
    3. 1.2 A Systematic Approach
    4. 1.3 Types of Microorganisms
    5. Summary
    6. Review Questions
      1. Multiple Choice
      2. Fill in the Blank
      3. Short Answer
      4. Critical Thinking
  3. 2 How We See the Invisible World
    1. Introduction
    2. 2.1 The Properties of Light
    3. 2.2 Peering Into the Invisible World
    4. 2.3 Instruments of Microscopy
    5. 2.4 Staining Microscopic Specimens
    6. Summary
    7. Review Questions
      1. Multiple Choice
      2. Fill in the Blank
      3. Short Answer
      4. Critical Thinking
  4. 3 The Cell
    1. Introduction
    2. 3.1 Spontaneous Generation
    3. 3.2 Foundations of Modern Cell Theory
    4. 3.3 Unique Characteristics of Prokaryotic Cells
    5. 3.4 Unique Characteristics of Eukaryotic Cells
    6. Summary
    7. Review Questions
      1. Multiple Choice
      2. True/False
      3. Fill in the Blank
      4. Short Answer
      5. Critical Thinking
  5. 4 Prokaryotic Diversity
    1. Introduction
    2. 4.1 Prokaryote Habitats, Relationships, and Microbiomes
    3. 4.2 Proteobacteria
    4. 4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria
    5. 4.4 Gram-Positive Bacteria
    6. 4.5 Deeply Branching Bacteria
    7. 4.6 Archaea
    8. Summary
    9. Review Questions
      1. Multiple Choice
      2. True/False
      3. Fill in the Blank
      4. Short Answer
      5. Critical Thinking
  6. 5 The Eukaryotes of Microbiology
    1. Introduction
    2. 5.1 Unicellular Eukaryotic Parasites
    3. 5.2 Parasitic Helminths
    4. 5.3 Fungi
    5. 5.4 Algae
    6. 5.5 Lichens
    7. Summary
    8. Review Questions
      1. Multiple Choice
      2. Fill in the Blank
      3. Short Answer
      4. Critical Thinking
  7. 6 Acellular Pathogens
    1. Introduction
    2. 6.1 Viruses
    3. 6.2 The Viral Life Cycle
    4. 6.3 Isolation, Culture, and Identification of Viruses
    5. 6.4 Viroids, Virusoids, and Prions
    6. Summary
    7. Review Questions
      1. Multiple Choice
      2. True/False
      3. Fill in the Blank
      4. Short Answer
      5. Critical Thinking
  8. 7 Microbial Biochemistry
    1. Introduction
    2. 7.1 Organic Molecules
    3. 7.2 Carbohydrates
    4. 7.3 Lipids
    5. 7.4 Proteins
    6. 7.5 Using Biochemistry to Identify Microorganisms
    7. Summary
    8. Review Questions
      1. Multiple Choice
      2. True/False
      3. Matching
      4. Fill in the Blank
      5. Short Answer
      6. Critical Thinking
  9. 8 Microbial Metabolism
    1. Introduction
    2. 8.1 Energy, Matter, and Enzymes
    3. 8.2 Catabolism of Carbohydrates
    4. 8.3 Cellular Respiration
    5. 8.4 Fermentation
    6. 8.5 Catabolism of Lipids and Proteins
    7. 8.6 Photosynthesis
    8. 8.7 Biogeochemical Cycles
    9. Summary
    10. Review Questions
      1. Multiple Choice
      2. True/False
      3. Matching
      4. Fill in the Blank
      5. Short Answer
      6. Critical Thinking
  10. 9 Microbial Growth
    1. Introduction
    2. 9.1 How Microbes Grow
    3. 9.2 Oxygen Requirements for Microbial Growth
    4. 9.3 The Effects of pH on Microbial Growth
    5. 9.4 Temperature and Microbial Growth
    6. 9.5 Other Environmental Conditions that Affect Growth
    7. 9.6 Media Used for Bacterial Growth
    8. Summary
    9. Review Questions
      1. Multiple Choice
      2. Matching
      3. Fill in the Blank
      4. Short Answer
      5. Critical Thinking
  11. 10 Biochemistry of the Genome
    1. Introduction
    2. 10.1 Using Microbiology to Discover the Secrets of Life
    3. 10.2 Structure and Function of DNA
    4. 10.3 Structure and Function of RNA
    5. 10.4 Structure and Function of Cellular Genomes
    6. Summary
    7. Review Questions
      1. Multiple Choice
      2. True/False
      3. Matching
      4. Fill in the Blank
      5. Short Answer
      6. Critical Thinking
  12. 11 Mechanisms of Microbial Genetics
    1. Introduction
    2. 11.1 The Functions of Genetic Material
    3. 11.2 DNA Replication
    4. 11.3 RNA Transcription
    5. 11.4 Protein Synthesis (Translation)
    6. 11.5 Mutations
    7. 11.6 How Asexual Prokaryotes Achieve Genetic Diversity
    8. 11.7 Gene Regulation: Operon Theory
    9. Summary
    10. Review Questions
      1. Multiple Choice
      2. True/False
      3. Fill in the Blank
      4. Short Answer
      5. Critical Thinking
  13. 12 Modern Applications of Microbial Genetics
    1. Introduction
    2. 12.1 Microbes and the Tools of Genetic Engineering
    3. 12.2 Visualizing and Characterizing DNA, RNA, and Protein
    4. 12.3 Whole Genome Methods and Pharmaceutical Applications of Genetic Engineering
    5. 12.4 Gene Therapy
    6. Summary
    7. Review Questions
      1. Multiple Choice
      2. True/False
      3. Fill in the Blank
      4. Short Answer
      5. Critical Thinking
  14. 13 Control of Microbial Growth
    1. Introduction
    2. 13.1 Controlling Microbial Growth
    3. 13.2 Using Physical Methods to Control Microorganisms
    4. 13.3 Using Chemicals to Control Microorganisms
    5. 13.4 Testing the Effectiveness of Antiseptics and Disinfectants
    6. Summary
    7. Review Questions
      1. Multiple Choice
      2. True/False
      3. Fill in the Blank
      4. Short Answer
      5. Critical Thinking
  15. 14 Antimicrobial Drugs
    1. Introduction
    2. 14.1 History of Chemotherapy and Antimicrobial Discovery
    3. 14.2 Fundamentals of Antimicrobial Chemotherapy
    4. 14.3 Mechanisms of Antibacterial Drugs
    5. 14.4 Mechanisms of Other Antimicrobial Drugs
    6. 14.5 Drug Resistance
    7. 14.6 Testing the Effectiveness of Antimicrobials
    8. 14.7 Current Strategies for Antimicrobial Discovery
    9. Summary
    10. Review Questions
      1. Multiple Choice
      2. True/False
      3. Fill in the Blank
      4. Short Answer
      5. Critical Thinking
  16. 15 Microbial Mechanisms of Pathogenicity
    1. Introduction
    2. 15.1 Characteristics of Infectious Disease
    3. 15.2 How Pathogens Cause Disease
    4. 15.3 Virulence Factors of Bacterial and Viral Pathogens
    5. 15.4 Virulence Factors of Eukaryotic Pathogens
    6. Summary
    7. Review Questions
      1. Multiple Choice
      2. Fill in the Blank
      3. Short Answer
      4. Critical Thinking
  17. 16 Disease and Epidemiology
    1. Introduction
    2. 16.1 The Language of Epidemiologists
    3. 16.2 Tracking Infectious Diseases
    4. 16.3 Modes of Disease Transmission
    5. 16.4 Global Public Health
    6. Summary
    7. Review Questions
      1. Multiple Choice
      2. Matching
      3. Fill in the Blank
      4. Short Answer
      5. Critical Thinking
  18. 17 Innate Nonspecific Host Defenses
    1. Introduction
    2. 17.1 Physical Defenses
    3. 17.2 Chemical Defenses
    4. 17.3 Cellular Defenses
    5. 17.4 Pathogen Recognition and Phagocytosis
    6. 17.5 Inflammation and Fever
    7. Summary
    8. Review Questions
      1. Multiple Choice
      2. Matching
      3. Fill in the Blank
      4. Short Answer
      5. Critical Thinking
  19. 18 Adaptive Specific Host Defenses
    1. Introduction
    2. 18.1 Overview of Specific Adaptive Immunity
    3. 18.2 Major Histocompatibility Complexes and Antigen-Presenting Cells
    4. 18.3 T Lymphocytes and Cellular Immunity
    5. 18.4 B Lymphocytes and Humoral Immunity
    6. 18.5 Vaccines
    7. Summary
    8. Review Questions
      1. Multiple Choice
      2. Matching
      3. Fill in the Blank
      4. Short Answer
      5. Critical Thinking
  20. 19 Diseases of the Immune System
    1. Introduction
    2. 19.1 Hypersensitivities
    3. 19.2 Autoimmune Disorders
    4. 19.3 Organ Transplantation and Rejection
    5. 19.4 Immunodeficiency
    6. 19.5 Cancer Immunobiology and Immunotherapy
    7. Summary
    8. Review Questions
      1. Multiple Choice
      2. Matching
      3. Fill in the Blank
      4. Short Answer
      5. Critical Thinking
  21. 20 Laboratory Analysis of the Immune Response
    1. Introduction
    2. 20.1 Polyclonal and Monoclonal Antibody Production
    3. 20.2 Detecting Antigen-Antibody Complexes
    4. 20.3 Agglutination Assays
    5. 20.4 EIAs and ELISAs
    6. 20.5 Fluorescent Antibody Techniques
    7. Summary
    8. Review Questions
      1. Multiple Choice
      2. Fill in the Blank
      3. Short Answer
      4. Critical Thinking
  22. 21 Skin and Eye Infections
    1. Introduction
    2. 21.1 Anatomy and Normal Microbiota of the Skin and Eyes
    3. 21.2 Bacterial Infections of the Skin and Eyes
    4. 21.3 Viral Infections of the Skin and Eyes
    5. 21.4 Mycoses of the Skin
    6. 21.5 Protozoan and Helminthic Infections of the Skin and Eyes
    7. Summary
    8. Review Questions
      1. Multiple Choice
      2. Fill in the Blank
      3. Short Answer
      4. Critical Thinking
  23. 22 Respiratory System Infections
    1. Introduction
    2. 22.1 Anatomy and Normal Microbiota of the Respiratory Tract
    3. 22.2 Bacterial Infections of the Respiratory Tract
    4. 22.3 Viral Infections of the Respiratory Tract
    5. 22.4 Respiratory Mycoses
    6. Summary
    7. Review Questions
      1. Multiple Choice
      2. Fill in the Blank
      3. Short Answer
      4. Critical Thinking
  24. 23 Urogenital System Infections
    1. Introduction
    2. 23.1 Anatomy and Normal Microbiota of the Urogenital Tract
    3. 23.2 Bacterial Infections of the Urinary System
    4. 23.3 Bacterial Infections of the Reproductive System
    5. 23.4 Viral Infections of the Reproductive System
    6. 23.5 Fungal Infections of the Reproductive System
    7. 23.6 Protozoan Infections of the Urogenital System
    8. Summary
    9. Review Questions
      1. Multiple Choice
      2. Fill in the Blank
      3. Short Answer
      4. Critical Thinking
  25. 24 Digestive System Infections
    1. Introduction
    2. 24.1 Anatomy and Normal Microbiota of the Digestive System
    3. 24.2 Microbial Diseases of the Mouth and Oral Cavity
    4. 24.3 Bacterial Infections of the Gastrointestinal Tract
    5. 24.4 Viral Infections of the Gastrointestinal Tract
    6. 24.5 Protozoan Infections of the Gastrointestinal Tract
    7. 24.6 Helminthic Infections of the Gastrointestinal Tract
    8. Summary
    9. Review Questions
      1. Multiple Choice
      2. Fill in the Blank
      3. Short Answer
      4. Critical Thinking
  26. 25 Circulatory and Lymphatic System Infections
    1. Introduction
    2. 25.1 Anatomy of the Circulatory and Lymphatic Systems
    3. 25.2 Bacterial Infections of the Circulatory and Lymphatic Systems
    4. 25.3 Viral Infections of the Circulatory and Lymphatic Systems
    5. 25.4 Parasitic Infections of the Circulatory and Lymphatic Systems
    6. Summary
    7. Review Questions
      1. Multiple Choice
      2. Fill in the Blank
      3. Short Answer
      4. Critical Thinking
  27. 26 Nervous System Infections
    1. Introduction
    2. 26.1 Anatomy of the Nervous System
    3. 26.2 Bacterial Diseases of the Nervous System
    4. 26.3 Acellular Diseases of the Nervous System
    5. 26.4 Fungal and Parasitic Diseases of the Nervous System
    6. Summary
    7. Review Questions
      1. Multiple Choice
      2. Matching
      3. Fill in the Blank
      4. Short Answer
      5. Critical Thinking
  28. A | Fundamentals of Physics and Chemistry Important to Microbiology
  29. B | Mathematical Basics
  30. C | Metabolic Pathways
  31. D | Taxonomy of Clinically Relevant Microorganisms
  32. E | Glossary
  33. Answer Key
    1. Chapter 1
    2. Chapter 2
    3. Chapter 3
    4. Chapter 4
    5. Chapter 5
    6. Chapter 6
    7. Chapter 7
    8. Chapter 8
    9. Chapter 9
    10. Chapter 10
    11. Chapter 11
    12. Chapter 12
    13. Chapter 13
    14. Chapter 14
    15. Chapter 15
    16. Chapter 16
    17. Chapter 17
    18. Chapter 18
    19. Chapter 19
    20. Chapter 20
    21. Chapter 21
    22. Chapter 22
    23. Chapter 23
    24. Chapter 24
    25. Chapter 25
    26. Chapter 26
  34. Index

Bacterial Pathogens

The following tables list the species, and some higher groups, of pathogenic Eubacteria mentioned in the text. The classification of Bacteria, one of the three domains of life, is in constant flux as relationships become clearer through sampling of genetic sequences. Many groups at all taxonomic levels still have an undetermined relationship with other members of the phylogenetic tree of Bacteria. Bergey’s Manual of Systematics of Archaea and Bacteria maintains a published list and descriptions of prokaryotic species. The tables here follow the taxonomic organization in the Bergey’s Manual Taxonomic Outline.1

We have divided the species into tables corresponding to different bacterial phyla. The taxonomic rank of kingdom is not used in prokaryote taxonomy, so the phyla are the subgrouping below domain. Note that many bacterial phyla not represented by these tables. The species and genera are listed only under the class within each phylum. The names given to bacteria are regulated by the International Code of Nomenclature of Bacteria as maintained by the International Committee on Systematics or Prokaryotes.

Phylum Actinobacteria
Class Genus Species Related Diseases
Actinobacteria Corynebacterium diphtheriae Diphtheria
Gardnerella vaginalis Bacterial vaginosis
Micrococcus Opportunistic infections
Mycobacterium bovis Tuberculosis, primarily in cattle
Mycobacterium leprae Hansen’s disease
Mycobacterium tuberculosis Tuberculosis
Propionibacterium acnes Acne, blepharitis, endophthalmitis
Table D1
Phylum Bacteroidetes
Class Genus Species Related Diseases
Bacteroidia Porphyromonas Periodontal disease
Prevotella intermedia Periodontal disease
Table D2
Phylum Chlamydiae
Class Genus Species Related Diseases
Chlamydiae Chlamydia psittaci Psittacosis
Chlamydia trachomatis Sexually transmitted chlamydia
Table D3
Phylum Firmicutes
Class Genus Species Related Diseases
Bacilli Bacillus anthracis Anthrax
Bacillus cereus Diarrheal and emetic food poisoning
Listeria monocytogenes Listeriosis
Enterococcus faecalis Endocarditis, septicemia, urinary tract infections, meningitis
Staphylococcus aureus Skin infections, sinusitis, food poisoning
Staphylococcus epidermidis Nosocomial and opportunistic infections
Staphylococcus hominis Opportunistic infections
Staphylococcus saprophyticus Urinary tract infections
Streptococcus agalactiae Postpartum infection, neonatal sepsis
Streptococcus mutans Tooth decay
Streptococcus pneumoniae Pneumonia, many other infections
Streptococcus pyogenes Pharyngitis, scarlet fever, impetigo, necrotizing fasciittis
Clostridia Clostridium botulinum Botulinum poisoning
Clostridium difficile Colitis
Clostridium perfringens Food poisoning, gas gangrene
Clostridium tetani Tetanus
Table D4
Phylum Fusobacteria
Class Genus Species Related Diseases
Fusobacteriia Fusobacterium Periodontal disease, Lemierre syndrome, skin ulcers
Streptobacillus moniliformis Rat-bite fever
Table D5
Phylum Proteobacteria
Class Genus Species Related Diseases
Alphaproteobacteria Anaplasma phagocytophilum Human granulocytic anaplasmosis
Bartonella henselae Peliosis hepatitis, bacillary angiomatosis, endocarditis, bacteremia
Bartonella quintana Trench fever
Brucella melitensis Ovine brucellosis
Ehrlichia chaffeensis Human monocytic ehrlichiosis
Rickettsia prowazekii Epidemic typhus
Rickettsia rickettsii Rocky Mountain spotted fever
Rickettsia typhi Murine typhus
Betaproteobacteria Bordetella pertussis Pertussis
Eikenella Bite-injury infections
Neisseria gonorrhoeae Gonorrhea
Neisseria meningitidis Meningitis
Spirillum minus (alt. minor) Sodoku (rat-bite fever)
Epsilonproteobacteria Campylobacter jejuni Gastroenteritis, Guillain-Barré syndrome
Helicobacter pylori Gastric ulcers
Gammaproteobacteria Aeromonas hydrophila Dysenteric gastroenteritis
Coxiella burnetii Q fever
Enterobacter Urinary and respiratory infections
Escherichia coli
Strains:
shiga toxin-producing (STEC) (e.g., O157:H7) also called enterohemorrhagic E. coli (EHEC) or verocytotoxin-producing E. coli (VTEC)
Foodborne diarrhea outbreaks, hemorrhagic colitis, hemolytic-uremic syndrome
Escherichia coli
Strain:
enterotoxigenic E. coli (ETEC)
Traveler’s diarrhea
Escherichia coli
Strain:
enteropathogenic E. coli (EPEC)
Diarrhea, especially in young children
Escherichia coli
Strain:
enteroaggregative E. coli (EAEC)
Diarrheal disease in children and travelers
Escherichia coli
Strain:
diffusely adherent E. coli (DAEC)
Diarrheal disease of children
Escherichia coli
Strain:
enteroinvasive E. coli (EPEC)
Bacillary dysentery, cells invade intestinal epithelial cells
Francisella tularensis Tularemia
Haemophilus ducreyi Chancroid
Haemophilus influenzae Bacteremia, pneumonia, meningitis
Klebsiella pneumoniae Pneumonia, nosocomial infections
Legionella pneumophila Legionnaire’s disease
Moraxella catarrhalis Otitis media, bronchitis, sinusitis, laryngitis, pneumonia
Pasteurella Pasteurellosis
Plesiomonas shigelloides Gastroenteritis
Proteus Opportunistic urinary tract infections
Pseudomonas aeruginosa Opportunistic, nosocomial pneumonia and sepsis
Salmonella bongori Salmonellosis
Salmonella enterica Salmonellosis
Serratia Pneumonia, urinary tract infections
Shigella boydii Dysentery
Shigella dysenteriae Dysentery
Shigella flexneri Dysentery
Shigella sonnei Dysentery
Vibrio cholerae Cholera
Vibrio parahemolyticus Seafood gastroenteritis
Vibrio vulnificus Seafood gastroenteritis, necrotizing wound infections, septicemia
Yersinia enterocolitica Yersiniosis
Yersinia pestis Plague
Yersinia pseudotuberculosis Far East scarlet-like fever
Table D6
Phylum Spirochaetes
Class Genus Species Related Diseases
Spirochaetia Borrelia burgdorferi Lyme disease
Borrelia hermsii Tick-borne relapsing fever
Borrelia recurrentis Louse-borne relapsing fever
Leptospira interrogans Leptospirosis
Treponema pallidum Syphilis, bejel, pinta, yaws
Table D7
Phylum Tenericutes
Class Genus Species Related Diseases
Mollicutes Mycoplasma genitalium Urethritis, cervicitis
Mycoplasma hominis Pelvic inflammatory disease, bacterial vaginosis
Mycoplasma pneumoniae Mycoplasma pneumonia
Ureaplasma urealyticum Urethritis, fetal infections
Table D8

Viral Pathogens

There are several classification systems for viruses. The International Committee on Taxonomy of Viruses (ICTV) is the international scientific body responsible for the rules of viral classification. The ICTV system used here groups viruses based on genetic similarity and presumed monophyly. The viral classification system is separate from the classification system for cellular organisms. The ICTV system groups viruses within seven orders, which contain related families. There is, presently, a large number of unassigned families with unknown affinities to the seven orders. Three of these orders infect only Eubacteria, Archaea, or plants and do not appear in this table. Some families may be divided into subfamilies. There are also many unassigned genera. Like all taxonomies, viral taxonomy is in constant flux. The latest complete species list and classification can be obtained on the ICTV website.2

A table titled “Viral Pathogens” gives information on order, family, subfamily, genus, species, and related diseases. For order Herpesvirales, family herpesviridae, subfamily betaherpesvirinae, genus human cytomegalovirus group, species human herpesvirus 5, the related disease is Cytomegalovirus hepatitis and other infections in immunocompromised people. For order herpesvirales, family herpesviridae, subfamily gammaherpesvirinae, genus lymphocryptovirus, species human herpesvirus 4(HHV-4; Epstein-Barr virus), the related disease is infectious mononucleosis. For order Herpesvirales, family herpesviridae, subfamily alphaherpesvirinae, genus simplexvirus, species human herpesvirus 1, human herpesvirus 2, the related diseases are herpes simplex virus 1, herpes simplex virus 2. For order herpesvirales, family herpesviridae, subfamily alphaherpesvirinae, genus varicellovirus, species human herpesvirus 3, the related diseases chickenpox, shingles. For order mononegavirales, family filoviridae, subfamily alphaherpesvirinae, genus ebolavirus, species zaire ebolavirus (EBOV), the related disease is Ebola. For order mononegavirales, family filoviridae, genus marburgvirus, species Marburg marburgvirus (MARV), the related disease is Marburg virus disease. For order mononegavirales, family rhabdoviridae, genus lyssavirus, species rabies virus, the related disease is Rabies. For order mononegavirales, family paramyxoviridae, subfamily pneumovirinae, genus pneumovirus, species human respiratory syncytial virus, the related disease is lower respiratory tract infection. For order mononegavirales, family paramyxoviridae, subfamily paramyxovirinae, genus morbillivirus, species measles virus, the related disease is measles (rubeola). For order Nidovirales, family coronaviridae, subfamily coronavirinae, genus coronavirus, the related diseases are common cold, pneumonia, SARS. For order picornavirales, family picornaviridae, genus hepatovirus, species hepatitis A virus, the related disease is hepatitis A. For order picornavirales, family picornaviridae, genus enterovirus, species enterovirus C, the related disease is polio. For order picornavirales, family picornaviridae, genus enterovirus, species rhinovirus A, the related disease is common cold. For order picornavirales, family picornaviridae, genus enterovirus, species rhinovirus B, the related disease is common cold. For order picornavirales, family picornaviridae, genus enterovirus, species rhinovirus C, the related disease is common cold. The remaining entries in this table are unassigned in the order category. In the family adenovirus, genus mastadenovirus, the related diseases are respiratory and other infections. In the family arenaviridae, genus mammarenavirus, species lassa mammarenavirus, the related disease is Lassa fever. For the family astroviridae, the related disease is gastroenteritis. For the family bunyaviridae, genus hantavirus, species several species, the related diseases are hantavirus hemorrhagic fever with renal syndrome (HFRS), hantavirus pulmonary syndrome (HPS). For family Bunyaviridae, genus nairovirus, species Crimean-congo hemorrhagic fever virus (CCHF), the related disease is Crimean-Congo hemorrhagic fever. For the family caliciviridae, genus norovirus, species Norwalk virus, the related disease is gastroenteritis.
Figure D1
A table titled “Viral Pathogens (continued)” gives information on order, family, subfamily, genus, species, and related diseases.All entries in this table are unassigned in the order category. For the family flaviviriadae, genus flavivirus, species dengue virus, the related disease is dengue fever. For the family flaviviriadae, genus flavivirus, species Yellow fever virus, the related disease is yellow fever. In the family flaviviriadae, genus hepacivirus, species hepatitis c virus, the related disease is hepatitis C. For the family hepadnaviridae, genus orthohepadnavirus, species hepatitis B virus, the related disease is hepatitis B. For the family Hepeviridae, genus orthohepevirus, species hepatitis E virus, the related disease is hepatitis E. For the family orthomyxoviridae, genus influenzavirus A, species influenza virus A, the related disease is pandemic flu. For the family orthomyxoviridae, genus influenzavirus B, species influenza virus B, the related disease is Flu. For the family orthomyxoviridae, genus influenzavirus C, species influenza virus C, the related disease is Flu. For the family papillomaviridae, genus alphapapillomavirus, species human papillomavirus, the related disease is skin warts. For the family parvoviridae, subfamily parvovirinae, genus erythroparvovirus, species human parvovirus B 19, the related disease is fifth disease (erythema infectosum). For the family poxviridae, subfamily chordopoxvirinae, genus orthopoxvirus, species variola virus, the related diseases are variola major, variola minor (smallpox). For the family poxviridae, subfamily chordopoxvirinae, genus orthopoxvirus, species vaccinia virus, the related disease is cowpox. For the family reoviridae, subfamily sedoreovirinae, genus rotavirus, species eight species, the related disease is gastroenteritis. For the family retroviridae, subfamily orthoretrovirinae, genus lentivirus, species human immunodeficiency virus, the related disease is AIDS. For the family togaviridae, genus alphavirus, species chikungunya virus (CHIKV), the related disease is Chikungunya. For the family togaviridae, genus rubivirus, species rubella virus, the related disease is Rubella (German measles). For an unassigned order, genus deltavirus, species hepatitis D virus, the related disease is hepatitis D.
Figure D2

Fungal Pathogens

The Fungi are one of the kingdoms of the domain Eukarya. Fungi are most closely related to the animals and a few other small groups and more distantly related to the plants and other groups that formerly were categorized as protist. At present, the Fungi are divided into seven phyla (or divisions, a hold over from when fungi were studied with plants), but there are uncertainties about some relationships.3 Many groups of fungi, particularly those that were formerly classified in the phylum Zygomycota, which was not monophyletic, have uncertain relationships to the other fungi. The one species listed in this table that falls into this category is Rhizopus arrhizus. Fungal names are governed by the International Code of Nomenclature for Algae, Fungi, and Plants,4 but the International Commission on the Taxonomy of Fungi (ICTF) also promotes taxonomic work on fungi. One activity of the ICTF is publicizing name changes for medically and otherwise important fungal species. Many species that formerly had two names (one for the sexual form and one for the asexual form) are now being brought together under one name.

Fungal Pathogens
Division Genus Species Related Diseases
Ascomycota Aspergillus flavus Opportunistic aspergillosis
Aspergillus fumigatus Opportunistic aspergillosis
Blastomyces dermatitidis Blastomycosis
Candida albicans Thrush (candidiasis)
Coccidioides immitis Valley fever (coccidioidomycosis)
Epidermophyton Tinea corporis (ringworm), tinea cruris (jock itch), tinea pedis (althlete’s foot), tinea unguium (onychomycosis)
Histoplasma capsulatum Histoplasmosis
Microsporum Tinea capitis (ringworm), tinea corpus (ringworm), other dermatophytoses
Pneumocystis jirovecii Opportunistic pneumonia
Sporothrix schenckii Sporotrichosis (rose-handler’s disease)
Trichophyton mentagrophytes var. interdigitale Tinea barbae (barber’s itch), dermatophytoses
Trichophyton rubrum Tinea corporis (ringworm), tinea cruris (jock itch), tinea pedis (althlete’s foot), tinea unguium (onychomycosis)
Basidiomycota Cryptococcus neoformans Opportunistic cryptococcosis, fungal meningitis, encephalitis
Malassezia Dandruff, tinea versicolor
uncertain Rhizopus arrhizus Mucormycosis
Table D9

Protozoan Pathogens

The relationships among the organisms (and thus their taxonomy) previously grouped under the name Protists are better understood than they were two or three decades ago, but this is still a work in progress. In 2005, the Eukarya were divided into six supergroups.5 The latest high-level classification combined two of the previous supergroups to produce a system comprising five supergroups.6 This classification was developed for the Society of Protozoologists, but it is not the only suggested approach. One of the five supergroups includes the animals, fungi, and some smaller protist groups. Another contains green plants and three algal groups. The other three supergroups (listed in the three tables below) contain the other protists, many of them which cause disease. In addition, there is a large number of protist groups whose relationships are not understood. In the three supergroups represented here we have indicated the phyla to which the listed pathogens belong.

Supergroup Amoebozoa
Phylum Genus Species Related Diseases
Amoebozoa Acanthamoeba Granulomatous amoebic encephalitis, acanthamoebic keratitis
Entamoeba histolytica Enterobiasis
Table D10
Supergroup SAR (Stramenopiles, Alveolata, Rhizaria)
Phylum Genus Species Related Diseases
Apicomplexa Babesia Babesiosis
Cryptosporidium hominis Cryptosporidiosis
Cryptosporidium parvum Cryptosporidiosis
Cyclospora cayetanensis Gastroenteritis
Plasmodium falciparum Malaria
Plasmodium malariae “Benign” or “quartan” (3-day recurrent fever) malaria
Plasmodium ovale “Tertian” (2-day recurrent fever) malaria
Plasmodium vivax “Benign” “tertian” (2-day recurrent fever) malaria
Plasmodium knowlesi Primate malaria capable of zoonosis, quotidian fever
Toxoplasma gondii Toxoplasmosis
Table D11
Supergroup Excavata
Phylum Genus Species Related Diseases
Metamonada Giardia lamblia Giardiasis
Trichomonas vaginalis Trichomoniasis
Euglenozoa Leishmania braziliensis Leishmaniasis
Leishmania donovani Leishmaniasis
Leishmania tropica Cutaneous leishmaniasis
Trypanosoma brucei African sleeping sickness (African trypanosomiasis)
Trypanosoma cruzi Chagas disease
Percolozoa Naegleria fowleri Primary amoebic meningoencephalitis (naegleriasis)
Table D12

Parasitic Helminths

The taxonomy of parasitic worms, all of which belong to the kingdom Animalia still contains many uncertainties. The pathogenic species are found in two phyla: the Nematoda, or roundworms, and the Platyhelminthes, or flat worms. The Nematoda is tentatively divided into two classes7, one of which, Chromadorea, probably contains unrelated groups. The parasitic flatworms are contained within three classes of flatworm, of which two are important to humans, the trematodes and the cestodes.

Phylum Nematoda
Class Genus Species Related Diseases
Chromadorea Ancylostoma caninum Dog hookworm infection
Ancylostoma duodenale Old World hookworm infection
Ascaris lumbricoides Ascariasis
Enterobius vermicularis Enterobiasis (pin worm)
Loa loa Loa loa filariasis (eye worm)
Necator americanus Necatoriasis (New World hookworm infection)
Strongyloides stercoralis Strongyloidiasis
Enoplea Trichinella spiralis Trichinosis
Trichuris trichiura Trichuriasis (whip worm infection)
Table D13
Phylum Platyhelminthes
Class Genus Species Related Diseases
Trematoda Clonorchis sinensis Chinese liver fluke
Fasciolopsis buski Fasciolopsiasis
Fasciola gigantica Fascioliasis
Fasciola hepatica Fascioliasis
Opisthorchis felineus Opisthorchiasis
Opisthorchis viverrini Opisthorchiasis
Schistosoma haematobium Urinary schistosomiasis
Schistosoma japonicum Schistosomiasis
Schistosoma mansoni Intestinal schistosomiasis
Cestoda Diphyllobothrium latum Diphyllobothriosis
Echinococcus granulosus Hydatid cysts (cystic echinococcosis)
Echinococcus multilocularis Echinococcosis
Taenia asiatica Intestinal taeniasis
Taenia saginata Intestinal taeniasis
Taenia solium Intestinal taeniasis, cysticercosis
Table D14

Footnotes

  • 1 Bergey’s Manual Trust. Bergey’s Manual of Systematics of Archaea and Bacteria, Taxonomic Outline. 2012. http://www.bergeys.org/outlines.html
  • 2 International Committee on Taxonomy of Viruses. “ICTV Master Species List.” http://talk.ictvonline.org/files/ictv_documents/m/msl/default.aspx
  • 3 D. S. Hibbett et al. “A Higher-level Phylogenetic Classification of the Fungi.” Mycological Research 111 no. 5 (2007):509–547.
  • 4 J. McNeill et al. International Code of Nomenclature for Algae, Fungi, and Plants (Melbourne Code). Oberreifenerg, Germany. Koeltz Scientific Books; 2012. http://www.iapt-taxon.org/nomen/main.php?
  • 5 S.M. Adl et al. “The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists.” Journal of Eukaryotic Microbiology 52 no. 5 (2005):399–451.
  • 6 S.M. Adl et al. “The Revised Classification of Eukaryotes.” Journal of Eukaryotic Microbiology 59 no. 5 (2012):429–514.
  • 7 National Center for Biotechnology Information. “Taxonomy Browser: Nematoda.” http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=6231
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