Infektiologie
aus
der Sicht der
interdisziplinären Infektionsmedizin
14.1 Koneman´s
Color Atlas and Textbook
of Diagnostic
Microbiology
6th Edition
Winn Jr. et al., Lippincott Williams & Wilkins
2006
Chapter 1: Introduction to
Microbiology
Part I: The Role of the Microbiology Laboratory in
the Diagnosis of Infectious Diseases:
Guidelines to
Practice and Management
Introduction
Outline of the
Book
The
World of Infectious Diseases
The
Triad of Infectious Diseases
The Infectious
Agent
Classes of Infectious Agents
Interactions Between Hosts and Infectius Agents
Purpose of Infectious
Agents in Nature
Virulence
The Environment
The
Infected Host
Innate Humoral (Noncellular) Defenses
Innate Cellulare
Defenses
Types of Inflammation
Adaptive Immunologic
Cellular Defenses
Adaptive Immunologic
Noncellular (Humoral) Defenses
Clinical Signs and
Symptoms of Infection
Indirect Effects of
Infectious Agents on Humans
Phases of the
Diagnostic Cycle
Preanalytic Phase
Specimen Collection
Specimen Transport
Specimen Receipt and
Preliminary Observations
Criteria for Rejection
of Specimens
Cost-Effective
Approaches in the Preanalytic Phase
Analytic Phase
Microscopic Examination
Processing Specimens
Interpretation of
Cultures
Procedures for
Preliminary Identification of Bacterial Isolates
Identification of
Organisms Other Than Bacteria
Testing of
Susceptibility to Antimicrobial Agents
Cost-Effective
Approaches in the Analytic Phase
Postanalytic
Phase
Reporting Results
Interactions With Epidemiologists
Analysis of Results
Maintenance of Samples
and Records
Administrative
Aspects of the Microbiology Laboratory
Government
Regulations
Risk
Management
Laboratory
Safety
General Safety Rules and Regulations
Routine Safety
Precautions
Biologic Agents
Universal Precautions
Shipping of Specimens
and Etiologic Agents
Nonbiologic Hazards
Bioterrorism
Quality Assurance
Quality Control
Components of a Quality
Control Program
Monitoring Laboratory
Equipment
Monitoring Culture
Media, Reagents, and Supplies
Chapter 2:
Introduction to Microbiology
Part II: Guidelines
for the Collection, Transport, Processing, Analysis and Reporting of Cultures
from Specific Specimen Sources
Infections
of the Respiratory Tract
Infections of the
Upper Respiratory Tract
Indigenous Flora
Pharyngitis
Infections of the Oral
Cavity Other Than Pharyngitis
Infections of the
Nasopharynx and Nasopharyngeal Cultures
Otitis Media and
Sinusitis
Epiglottitis
Laryngitis
Other Infections of the
Upper Respiratory Tract
Infections of the
Lower Respiratory Tract
Tracheobronchitis
Bronchiolitis
Pneumonia
Chronic Pneumonia
Empyema
Pneumonia in Special
Populations
Collection of Specimens
for the Diagnosis of Lower Respiratory Infection
Laboratory Diagnosis of
Pneumonia
Infections
of the Gastrointestinal Tract
Lower Intestinal
Infections
Clinical Symptoms
Collection of Fecal
Specimens
Epidemiologic
Considerations in the Evaluation of Patients With
Gastroenteritis
Upper Intestinal
Infections
Clinical Symptoms
Obtaining Specimens From the Upper Gastrointestinal Tract
Urinary
Tract Infections
Clinical Signs and
Symptoms
Host
Factors
Collection
of Urine Samples for Culture
Midstream Urine
Specimens
Other Voided Urine
Specimens
Catheter Collections
Suprapubic Aspiration
Culture of Urine
Specimens
Screening
Tests for Urinary Tract Infection
Screening Tests for
Bacteriuria
Screening Tests for
Pyuria
Infections
of the Genital Tract
Sexually
Transmitted Infections
Urethritis and Cervicits
Genital Ulcer Disease
Genital Infections
Transmitted by Nonsexual Means
Vaginitis and Vaginosis
Infections of the Upper
Female Genital Tract
Systemic
Complications of Genital Infections
Diagnosis
of Genital Tract Infections
Diagnosis of Urethritis,
Cervicitis, and Vaginitis
Diagnosis of Genital
Ulcer Disease and Venereal Warts
Collection of Genital
Specimen
Infections
of the Bones and joints
Clinical
Presentation
Diagnosis
of Infections of the Bones and Joints
Infections
of the Central Nervous System
Meningitis
Encephalitis and
Brain Abscess
Diagnosis of
Central Nervous System Infections
Collection
of Specimens
Assessing
the Inflammatory Response and Microscopic Techniques
Direct
Detection of Antigen and Nucleic Acid
Serologic
Diagnosis
Diagnosis
by Culture
Wounds,
Abscessed, and Cellulitis
Clinical
Presentation
Diagnosis
of Wound Infections, Abscesses, and Cellulitis
Collection of
Specimens
Microscopic
Examination of Specimens
Culture
Eye
Infections
Clinical
Presentation
Conjunctivitis
Keratitis
Uveitis and
Endophthalmitis
Diagnosis of Eye
Infections
Collection of
Specimens
Microscopic
Examination
Culture
Infections
of the Blood
Clinical
Presentation and Pathogenesis
Bacteremia
and Septicemia
Types of
Bacteremia
Intravascular
Infection
Catheter-Associated
Bacteremia and Sepsis
Collection of
Blood Cultures
Contamination
With Skin Flora
Number and
Timing of Cultures
Culture Media
Systems for
Processing Blood Cultures
Manual Blood
Culture Systems
Lysis-Centrifugation
Blood Culture System
Automated and
Computerized Blood Culture Systems
Comperative
Studies
Special
Considerations
Fastidious
Organisms and Endocarditis
Catheter-Associated
Bacteremia and Sepsis
Tissues and
Biopsies
Chapter 3: Laboratory Diagnosis by Immunologic Methods
Antigens
and Antibodies: Basic definitions
Monoclonal
antibodies
types
of antigen-antibody reactions used in diagnostic serology
Precipitin
Reactions
Complement
Fixation and Hemagglutination Inhibition
Agglutination
Reactions
solid-phase
immunoassay methods
Enzyme
Immunoassays for Antibody Detection
Enzyme
Immunoassay Antibody Capture Methods for IgM Detection
Enzyme
Immunoassays for Antigen Detection
immunofluorescence
techniques
Immunofluorescence
Techniques for Antigen Detection
Immunofluorescence
Techniques for Antibody Detection
Chapter
4: Molecular Microbiology
Nucleid
Acids – the basics of DNA and RNA
Structure
of DNA
Structure
of RNA
Function
of DNA-Information Storage
Function
of RNA-Information Transfer
Signal-amplification
methods
Nucleic-Acid
Probes
Clinical Applications
Hybrid
Capture
Clinical Applications
Branched
DNA
Clinical Applications
In
Situ Hybridization
Clinical Applications
Nucleic-acid
Amplification
Basics
of the Polymerase Chain Reaction
Clinical Applications
Other Methods of
Nucleic-Acid Amplification
Clinical Applications
Modifications of
PCR
RT-PCR
Clinical Applications
Broad-Range PCR
Clinical Applications
Multiplex PCR
Clinical Applications
Nested PCR
Clinical Applications
Postamplification
analysis
Traditional
Methods of Detection
Gel
Electrophoresis/Southern Blot Analysis
Enzymatic Detection
of Amplified Products
Clinical
Applications
Reverse
Hybridization
Clinical
Applications
DNA Sequencing
Traditional
DNA Sequencing
Clinical
Applications
Sequencing by
Synthesis (Pyrosequencing)
Clinical
Applications
Microarray
Analysis
Clinical
Applications
Real-time
nucleic-acid amplifications
Methods of
Detecting the Products of Real-Time Amplification
SYBR Green
Hybridization
Probes
Clinical
Applications
Strain
typing
Non-Amplification-Based
Typing
Pulsed-Field
Gel Electrophoresis
Amplification-Based
Typing
PCR-RFLP
Rep-PCR
Clinical
Applications of Microbial Typing
Conclusion
Chapter 5: Medical Bacteriology: Taxonomy, Morphology, Physiology, and Virulence
Taxonomy:
Classification, Nomenclature, and identification of bacteria
The Naming of
Bacteria
Phenotypic
Identification of Bacteria
Phylogenetic
Criteria for Classification of Bacteria
Basic
Bacterical anatomy and physiology
Bacterial Size and
Shape
Nuclear
Structure, DNA Replication, Transcription, and Translation
Cytoplasm
Cytoplasmic
Membrane
Bacterial
Cell Wall Structure
Gram-Positive
Bacterial Cell Walls
Gram-Negative
Bacterial Cell Walls
“Acid-Fast”
Bacterial Cell Walls
Bacterial
Endospores
Bacterial Surface Structures
Capsules
Flagella
Fimbriae
(Pili)
Genetic Exchange
and Recombination in Bacteria
Requirements
for Bacterial Growth and Metabolism
Carbon
Carbon
Dioxide
Oxygen
Nitrogen
Growth
Factors
Kinetics of Bacterial
Cell Growth
General
Bacterial Metabolism and Energy Generation
Fermentation
Utilization
of Pyruvate
Bacterial
virulence factors and pathogenicity
Definitions and
Concepts
Requirements for
Pathogenicity
Virulence Factors
of Microorganisms
Adhesins
Aggressins
Exotoxins
and Endotoxins
Bacterial
Superantigens
Chapter 6: The Enterobacteriace
Characteristics
for presumptive identification
Screening
Characteristics
Carbohydrate
Utilization
Cytochrome
Oxidase Activity
Nitrate Reduction
culture
media used for detection of carbohydrate fermentation
Use of Kligler
Iron Agar and Triple Sugar Iron Agar
Biochemical
Principles
selection
of primary isolation media
Chemicals and
Compounds Used in Selective Media
Selective
Isolation Media
Highly Selective
Isolation Media Used Primarily for Gastrointestinal Specimens
Enrichment Media
Guidelines for
Choosing Selective Isolation Media
Differential
identification characteristics
Indole
Production
Methyl
Red Test
Voges-Proskauer
Test
Citrate
Utilization
Urease
Production
Decarboxylation
of Lysine, Ornithine, and Arginine
Phenylalanine
Deaminase Production
Hydrogen
Sulfide Production
Motility
Taxonomy
of the enterobacteriaceae
Classification
of Enterobacteriaceae by Tribes
Key Identification
Characteristics for the Most Common Species
Tribe
Escherichieae
Tribe
Edwarsielleae
Tribe
Salmonelleae
Tribe
Citrobactereae
Tribe
Klebsielleae
Tribe
Proteeae
Tribe
Yersinieae
Tribe
Erwinieae
Miscellaneous New Genera
of Enterobacteriaceae
Identification
Characteristics of Newer Enterobacteriaceae
Clinical
Significance of Newer Enterobacteriaceae
Quick
screening methods for rapid identification
Commercial
Screening Kits
Chromogenic Agar
Media
Classic
identification systems
Checkerboard
Matrix
Branching Flow
Diagrams
Computer-Aided
Schemes
Numeric
conding systems
Estimated
Frequency of Occurrence
Calculation
of Likelihood
Resolving
Discrepancies
Packaged
kit identification systems
Overview
of Packaged Systems
Specific
Identification Systems
API 20E
BBL Crystal
Enteric/Nonfermenter ID Systems
RapID onE
System
Enterotube II
Micro-ID
Biolog GN2
Microplate
MicroScan
System
Sensititre
System
Semiautomated
and automated identfication systems
MicroScan
Walaway
Vitek
System
Sensititre
Gram-Negative AutoIdentification System
The
The
OmniLog ID System
Chapter
7: The Nonfermentative Gram-Negative Bacilli
Part I: Metabolism of the Nonfermenters
Fermentative
and oxidative metabolism
The
Embden-Meyerhof-Parnas Pathway
The
Entner-Doudoroff Pathway
The
Warburg-Dickens Hexose Monophosphate Pathway
initial
clues that an unknown isolate is a nonfermenter
Lack of Evidence for Glucose
Fermentation
Positive
Cytochrome Oxidase Reaction
Failure
to Grow on MacConkey Agar
tests
used in the identification of nonfermenters
Utilization of
Glucose
Motility
Pigment
Production
Hydrolysis
of Urea
Nitrate
Reduction
Denitrification
of Nitrates and Nitrites
Indole Production
Decarboxylation
Esculin
Hydrolysis
Flagella
Stains
Leifson Method
Ryu Method
Wet-Mount
Technique
Flagellar
Morphology
Part II: Taxonomy, Biochemical
Characteristics, and Clinical Significance of medically important genera
of nonfermenters
Organisms
that are motile with polar flagella
Pseudomonads
Family
Pseudomonadaceae
Genus Pseudomonas – rRNA Group I
Family
Burholderiaceae
rRNA Group II
Genus
Burkholderia – Pseudomallei Group
Genus Ralstonia and Genus Cupriavidus
Genus
Pandoraea
Genus
Inquilinus
Genua Lautropia
Family
Comamonadaceae
rRNA Group III
Acidovorans
Group
Facilis-Delafieldii
Group
Family
Caulobacteriaceae
rRNA Group IV
Brevundimonas-Diminuta
Group
Family
Xantomonadaceae
rRNA Group V
Genus
Stenotrophomonas
Family
Sphingomonadaceae
Genus Sphingomonas
Family
Oceanospirillaceae
Genus Balneatrix
Family
Oxalobacteraceae
Genus Massilia
Genus Herbaspirillum
Family
Alteromonadaceae
Genus Shewanella –
Hydrogen Sulfide-Producing Group
Genus Alishewanella – Halophilic Group
Family
Halomonadaceae
Genus Halomonas
Family
Methylobacteriaceae
Genus Methylobacterium
Genus Roseomonas
Unnamed Specied
Laribacter hongkongensis
Organisms
that are motile with peritrichous flagella
Family Alcaligenaceae
Genus
Alcaligenes
Genus
Achromobacter
Genus
Bordetella
Genus
Kerstersia
Genus
Oligella
Family Rhizobiaceae
Genus
Rhizobium (Formerly Agrobacterium)
Family
Brucellaceae
Genus Ochrobactrum
organisms
that are nonmotile and oxidase-positive
Family
Flavobacteriaceae
Chryseobacterium,
Empedobacter, and Unnamed CDC Groups
Weeksella and Bergeyella
Genus Myroides
Family
Sphingobacteriaceae
Sphingobacterium and
Pedobacter
Family
Moraxellaceae
Genus Moraxella
Genus Psychrobacter and
CDC EO Groups
Family
Neisseriaceae
Genus Neisseria
Gilardi Rod Group 1
organisms
that are nonmotile and oxisade-negative
Genus Acinetobacter
CDC Group NO-1
Bordetella holmesii (CDC
Group NO-2)
CDC Group EO-5
Part III: Approach to Recovery and
Identification of Nonfermenters
levels
of service in identification of nonfermenters
Guidelines
for recovery of nonfermenters
identification
of most common species
Pseudomonas
aeruginosa
Acinetobacter
baumannii
Stenotrophomonas
maltophilia
methods
for identification using conventional tests
Weyant
(CDC), Gilardi, and Pickett Identification Schemes
Practical
Approach to Identification of Nonfermenters
Computer-Aided
Schmes
commercial
kit systems
The
Oxi/Ferm Tube
The
API 20E System
The API 20NE
System
The Remel N/F
System
The Chrystal
Enteric/Nonfermenter System
The RapID NF Plus System
The Biolog System
automated
identification systems
The
Vitek Legacy System
The
Vitek 2 System
The
Microscan Walkaway-96, Walkaway-40, and Autoscan-4 Systems
The
Sensititre AP80 System
The
selection
of a System
Chapter 8: Curved
Gram-Negative Bacilli and Oxidase-Positive Fermenters:
Campylobacteraceae and Vibrionaceae
Part I: Curved Rods: Campylobacter,
Wolinella, Arcobacter Helicobacter, and Related Bacteria
historical
background
Classification
of campylobacter and related taxa
Campylobacter
Species
Campylobacter jejuni Subsp. jejuni
Other Campylobacter
Species
Former Wolinella and
Bacteroides Species Included in the Family Campylobacteraceae
Genus Arcobacter
Genus
Helicobacter
H. pylori
Other Medically
Important Helicobacter Species
Nonhuman Helicobacter
Species
Other Microaerophilic
Gram-Negative Bacilli
definitive
identification of campylobacters and related bacteria
Rapid
Identification of Campylobacters From Colonies and
From Stool Specimens
Nonculture Tests
Direct Detection Methods
Culture and
Isolation of Helicobacter pylori
Specimens for Recovery
of H. pylori
Isolation Procedure
Identification of H.
pylori
Biopsy Urease Test (CLO
Test)
Noninvasive Tests To Diagnose H. pylori Infection
Accuracy of Invasive and
Noninvasive Tests To Diagnose H. pylori Infection
Enterohepatic
Helicobacters
Part II: The Families Vibrionaceae and
Aeromonadaceae
Phylogeny
of the vibrionaceae
Genus Vibrio
Taxonomy
Description
and Associated Clinical Syndromes of Vibrio Species of Human Importance
Methods for Laboratory
Isolation of Vibrios
Biochemical
Characterization and Laboratory Identification of Vibrio Species
genera
listonella, photobacterium and shewanella
aeromonas
and plesiomonas
Genus aeromonas
Taxonomy
Clinical Significance
Aeromonas Species in
Medicinal Leeches
Laboratory Recovery of
Aeromonas Species From Clinical Specimens
Laboratory
Identification of Aeromonas Species
Genus Plesiomonas
Laboratory Isolation and
Identification
genus
chromobacterium
Chapter 9:
Miscellaneous Fastidious Gram-Negative Bacilli
haemophilus
species
Taxonomy of
Haemophilus and Related Organisms
Haemophilus
influenzae
Haemophilus
influenzae Type B Vaccines
Infections
Caused by Haemophilus Species
Meningitis
Epiglottitis
Otitis Media
Sinusitis
Bronchitis and Chronic
Obstructive Pulmonary Disease
Pneumonia
Bacteremia and
Infectious Complications of Bacteremia
Endocarditis
Urogential, maternal,
and Perinatal Infections
Ocular Infections
Brazilian Purpuric Fever
Miscellaneous
Haemophilus influenzae infections
Haemophilus
parainfluenzae
Haemophilus
aphrophilus and Haemophilus paraphrophilus
Other
Haemophilus Species
Haemophilus
ducreyi
Laboratory
Diagnosis of Haemophilus Infections
Direct Examination of
Clinical Specimens
Culture of Haemophilus
Species
Identification of
Haemophilus Species
Laboratory
Diagnosis of Haemophilus ducreyi Infection
Antimicrobial
Susceptibility of Haemophilus Species
actinobacillus
species
Actinobacillus
actinomycetemcomitans
Clinical Significance
Cultural Characteristics
and Identification
Antimicrobial
Susceptibility
Actinobacillus
ureae
Actinobacillus
hominis
Animal
Species in the Genus Actinobacillus
pasteurella
and mannheimia species
Taxonomy and
Characteristics of the Genus Pasteurella
Pasteurella
multocida
Clinical
Significance and Virulence
Cultural
Characteristics and Identification
Antimicrobial
Susceptibility
Other Pasteurella
Species Isolated From Human Infections
Pasteurella
pneumotropica (“Actinobacillus pneumotropica”)
Pasteurella
aerogenes (“Actinobacillus aerogenes”)
Pasteurella dagmatis
Pasteurella
canis and Pasteurella stomatis
Pasteurella bettyae
Pasteurella
caballi
Pasteurella
gallinarum
Mannheimia Species
(Formerly the « Pasteurella
haemolytica/Pasteurella granulomatis » Complex)
Cardiobacterium
hominis
Taxonomy
Clinical
Significance
Cultural
Characteristics and Identification
Antimicrobial
Susceptibility
eikenella
corrodens
Taxonomy
and Virulence
Clinical
Significance
Cultural
Characteristics and Identification
Antimicrobial
Susceptibility
kingella
and suttonella species
Taxonomy
Clinical
Significance
Cultural
Characteristics and Identification
Antimicrobial
Susceptibility
human
capnocytophaga species
Taxonomy
Clinical
Significance
Cultural
Characteristics and Identification
Antimicrobial
Susceptibility
canine
Capnocytophaga Species
Taxonomy
Clinical
Significance
Cultural
Characteristics and Identification
Antimicrobial
Susceptibility
dysgonomonas
species
cdc
groups EF-4A and EF-4B
Simosiella
Species
Streptobacillus
moniliformis
Taxonomy
Clinical
Significance
Cultural
Characteristics and Identification
Antimicrobial
Susceptibility
Brucella
species
Epidemiology
of Brucellosis
Taxonomy
of Brucella Species
Virulence
of Brucella Species
Clinical
Spectrum of Brucellosis
Serologic
Diagnosis of Brucellosis
Isolation
and Cultural Characteristics
Identification
of Brucella Species
Treatment
of Brucellosis
Francisella
tularensis
Epidemiology of
Tularemia
History and
Taxonomy
Virulence
of F. tularensis
Clinical
Spectrum of Tularemia
Isolation
and Cultural Characteristics
Serologic
Diagnosis of Tularemia
Treatment
Tularemia
bartonella
species
Taxonomy
and Epidemiology of Bartonella Species
Clinical
Significance of Bartonella Species
Oroya Fever and Verruga Peruana
« Classical »
and « Urban » Trench Fever
Bacillary
Angiomatosis
Peliosis
Fever
and Bacteremia
Endocarditis
Cat-Scratch
Disease (CSD)
Miscellaneous
Infections
Detection,
Isolation, and Identification of Bartonella Species
Specimen
Types
Culture
Gram
Stein and Colony Morphology
Identification
Methods
Serologic
Diagnosis of Bartonella Infections
In Vitro
Antimicrobial Susceptibility
Afipia
species
Taxonomy and
Clinical Significance
Isolation and
Identification
Antimicrobial
Susceptibility
bordetella
species
Background and Taxonomy
of Bordetella Species
Epidemiology of
Pertussis
Clinical
Significance of Bordetella pertussis
Pertussis Vaccines
Clinical
Significance of Other Bordetella Species
Bordetella
parapertussis
Bordetella
brochiseptica
Bordetella hinzii
Bordetella holmesii
Bordetella trematum
Isolation
and Identification of Bordetella Species
Specimens and Culture Media
Direct Fluorescent Antibody Test
Cultural Characteristics and Identification
New Technologies
for Detection and Identification of Bordetella pertussis
Serologic Tests For Diagnosis of Pertussis
Treatment of
Pertussis
Antimicrobial
Susceptibility Testing of Bordetella Species
Chapter 10: Legionella
taxonomy
and characteristics of the genus legionella
clinical
and pathologic spectrum of Legionellosis
Predisposing
Factors
Pathology and
Pathogenesis
epidemiologica
and ecologic aspects of legionellosis
Incidence
Legionellaceae in
the Environment
Natural Habitats
Man-Made (Artificial) Aquatic Habitats
Legionellosis in
Travelers
Nosocomial
Outbreaks of Legionellosis
laboratory
diagnosis
Selection,
Collection, and Transport of Clinical Specimens
Direct Examination
of Clinical Specimens
Gross Examination and Microscopic Examination of
Stained Materials
Microscopic Examination of Stained Materials
Direct Fluorescent Antibody (DFA) Procedure
Antigen Detection in Urine and Body Fluids
detection
of legionella in clinical specimens
Isolation of
Legionella Species From Clinical Specimens
Biopsy, Surgical Removal, and Autopsy Tissue
Pleural Fluid and Transtracheal Aspirates
Acid-Wash Decontamination Procedure for Sputum and
Other Contaminated Specimens
Blood Cultures
Identification of
Legionella Species
Antimicrobial
Susceptibility and Treatment
Serum Indirect
Immunofluorescent Antibody Test
Molecular
Diagnosis
environmental
microbiology studies
Isolation of
Legionella From Environmental Samples
Typing of
Legionella Isolates
Chapter
11: Neisseria Species and Moraxella catarrhalis
taxonomy of the
family Neisseriaceae and the family moraxellaceae
general characteristics
of the genus neisseria
clinical
significance of neisseria species
Neisseria
gonorrhoeae
Epidemiology
Infections Caused by N. gonorrhoeae
Neisseria
meningitidis
Epidemiology
Infections Caused by N. menigitidis
Meningococcal Prophylaxis and Meningococal Vaccines
Other Neisseria
Species
clinical
significance of moraxella catarrhalis
isolation of
neisseria species
Neisseria
gonorrhoeae
Direct
Gram-Stained Smears
Specimen
Collection
Specimen
Transport
Selective Culture
Media: Inoculation and Incubation
Neisseria meningitidis
Laboratory
Safety
Direct
Gram-Stained Smears and Direct Capsular Antigen Tests
Specimen Collection and
Transport
Isolation and Incubation
identification of
neisseria species
Colony Morphology
Gram
Stain and Oxidase Test
Superoxol
Test
Differentiation
of Other Organisms on Selective Media
Presumptive
Criteria for Identification of N. gonorrhoeae
Identification
Tests for Neisseria Species
Carbohydrate-Utilization
Tests
Conventional
CTA Carbohydrates
Rapid
Carbohydrate-Utilization Test
RIM-Neisseria
Test (Rapid Identification Method-Neisseria)
Other
Carbohydrate-Utilization Methods
Chromogenic Enzyme
Substrate Tests
Gonochek
II
BactiCard
Neisseria
Immunologic
Methods for Culture Confirmation of N. gonorrhoeae
Direct
Fluorescent Monoclonal Antibody Test
Coagglutination Tests
GonoGen II Test
Multitest
Identification Systems
DNA Probe Test for
Culture Confirmation of N. gonorrhoeae
Nucleic Acid Hybridization
and Amplification Tests for N. gonorrhoeae
Molecular Methods
for Detection of N. meningitidis
cultural
charactistics of Neisseria Species
Neisseria
gonorrhoeae
Neisseria
meningitidis
Other Neisseria
Species
Neisseria
lactamica
Neisseria
cinerea
Neisseria
flavescens
Neisseria
sublava Biovars, Neisseria mucosa, and Neisseria sicca
Neisseria
polysaccharea
Neisseria
elongata Subspecies
Neisseria
gonorrhoeae Subspecies kochii (“Neisseria kochii”)
Atypical and Non-Human Neisseria Species
cultural
characteristics and identification of moraxella catarrhalis
antimicrobial
susceptibility of neisseria species
Neisseria
gonorrhoeae
Neisseria
meningitidis
antimicrobial
susceptibility of moraxella catarrhalis
Chapter
12: Gram-Positive Cocci
Part I: Staphylococci and Related Gram-Positive Cocci
taxonomy of
Staphylococci and related gram-positive cocci
clinical
significance of staphylococci and related gram-positive cocci
Staphylococcus aureus
Subsp. aureus
Coagulase-Negative
Staphylococci
Staphylococcus
epidermidis
Staphylococcus
saprophyticus Subsp. saprophyticus
Other Coagulase-Negative Staphylococci
Micrococcus
Species and Related Genera
Rothia
mucilaginosa
isolation and
preliminary differentiation of staphylococci and related gram-positive cocci
Direct
Gram-Stained Smears
Isolation from
Clinical Specimens
Colony Morphology
The Catalase Test
Methods for
Differentiating Micrococci and Staphylococci
Fermentation of Glucose
Susceptibility to
Lysostaphin
Production
of Acid From Glycerol in the Presence of Erythromycin
Susceptibility
to Furazolidone
Modified
Oxidase Test
Susceptibility
to Bacitracin
identification of
staphylococcus aureus
Slide Coagulase
Test
Tube Coagulase
Test
Alternative Coagulase
Test Procedures
Latex
Agglutination
Passive
Hemagglutination
Additional
Confirmatory Tests
Deoxyribonuclease
(DNase) Test
Thermostable
Endonuclease Test
Mannitol
Fermentation
Other Methods for
Identification of Staphylococcus aureus
Rapid Tests for
Detection of Methicillin Resistance
Differentiation of
Coagulase-Positive Staphylococci of Veterinary Origin
identification of
coagulase-negative staphylococci
Conventional
Identification Methods
Production of Phosphatase for Identification of
Staphylococcus epidermidis
Pyrrolidonyl
Arylamidase Activity
Susceptibility
to Polymyxin B
Ornithine
Decarboxylase Test (ODC)
Urease
Production
Acetoin
Production
Susceptibility
to Deferoxamine
Susceptibility to
Novobiocin for Identification of Staphylococcus saprophyticus
Commercial
Identification Systems
RapiDEC Staph
API Staph-IDENT
API Staph
API ID32 Staph
Vitek Gram-Positive
Identification (GPI) Card
MicroScan Rapid Pos
Combo Panel
MicroScan Pos ID Panel
BBL Crystal
Gram-Positive (GP) Identification System
Staf-Sistem 18-R
Staph-Zym
Microbact Staphylococcal
12S
Microbial Identification
System
Biolog Microplate
Identification System
Molecular
Identification and Typing Methods for Staphylococci
Identification
of Micrococcus and Related Species
Identification
of Rothia mucilaginosa
laboratorY
approach to the identification of staphylococci
Chaper 13:
Gram-positive Cocci
Part II: Streptococci, Enterococci, and the
“Streptococcus-Like” Bacteria
general
characteristics of the streptococci
group A b-hemolytic streptococci (Streptococcus pyogenes)
Virulence Factors
Clinical
Significance
group B b-hemolytic streptococci (Streptococcus agalactiae)
Virulence
Factors
Clinical
Significance
group C and group
G b-hemolytic streptococci
group F b-hemolytic streptococci
other streptococci
in the “pyogenic cocci” group
Streptococcus
pneumoniae
Virulence Factors
Pneumococcal
Vaccines
Clinical
Significance
Viridans
Streptococci
the angionosus group:
Streptococcus angionosus, streptococcus constellatus, and Streptococcus
intermedius
group D
streptococci: the “streptococcus bovis/streptococcus equinus complex” and
related species
streptococcus suis
other viridans
streptococci isolated from animals
miscellaneous
streptococci
enterococcus
species
Taxonomy
Viruelence
Factors
Clinical
Significance
Genus
Melissococcus
the
“streptococcus-like” bacteria
Abiotrophia
and Granulicatella Species
Aerococcus
and Helcococcus Species
Leuconostoc
Species
Pediococcus
and Tetragenococcus Species
Gemella
Species
Vagococcus
Species
Alloiococcus
Species
Globicatella
Species
Facklamia
Species
Dolosigranulum,
Ignavigranum, and Dolosicoccus Species
Eremococcus
Species
Genus
Lactococcus
isolation and identification
of streptococci and “streptococcus-like” bacteria
Direct
Gram-Stained Smears
Culture
Media
Hemolysis
on Blood Agar
Nonculture, Direct Detection Techniques for Group A b-Hemolytic Streptococci in Pharyngeal Specimens
Nonculture, Direct Detection Techniques for Group B b-Hemolytic Streptococci and Streptococcus pneumoniae
Colony Morphology
and Catalase Testing
Recognition
and Preliminary Characterization of Streptococci and the “Streptococcus-Like”
Bacteria
Presumptive
Identification of Streptococci
Susceptibility to Bacitracin
Susceptibility to
Sulfamethoxazole-Trimethoprim (SXT)
Hydrolysis of Sodium
Hippurate
Bile-Esculin-Test
Salt-Tolerance Text (6,5 % NaCl Broth)
Leucine
Aminopeptidase (LAP) Test
Pyrrolidonyl
Arylamidase (PYR) test
Susceptibility
to Optochin
Bile-Solubility
Test
Commercial
Presumptive Identification Tests
Serologic
Identification of b-Hemolytic
Streptococci
Capillary
Precipitin Test
Coagglutination
Latex
Agglutination
Serologic
Identification of Streptococcus pneumoniae
Biochemical
Characteristics for Identification of Groupable Streptococci
Identification of
the Viridans Streptococci
Sanguis
Group
Mitis
Group
Mutans
Group
Salivarius
Group
Anginosus
Group
Bovis
Group
Identification of
Streptococcus suis and Other Streptococci Isolated
from Animals
Identification of
Enterococcus Species
Identification of
Abiotrophia and Granulicatella Species
Identification of
Aerococcus and Helcococcus Species
Identification of
Leuconostoc, Pediococcus, and Tetraggenococcus Species
Identification of
Gemella Species
Identification of
Vagococcus Species
Identification of
Alloiococcus, Globicatella, Facklamia, Dolosigranulum, Ignavigranum, and
Dolosicoccus Species
Identification of
Lactococcus Species
Commercially
Available Systems for Identification of Streptococci, Enterococci, and Selected
“Streptococcus-Like” Bacteria
API
Rapid Strep
BBL
Crystal Gram-Positive Identification System
RAPID
ID 32 Strep
RapID
STR
Vitek
Gram-Positive Identification (GPI) Card
Microscan
Gram-Positive Breakpoint Combo Panel
Chapter
14: Aerobic and Facultative Gram-Positive Bacilli
listeria species
and listeria monocytogenes
Taxonomy of the
Genus Listeria
Virulence Factors
of L. monocytogenes
Epidemiology of L.
monocytogenes
Clinical
Significance of L. monocytogenes
Isolation of L.
monocytogenes From Clinical Specimens
Identification of
Listeria Species
Antimicrobial
Susceptibility and Tratment of Listeria Infections
Pathogenicity of
Other Listeria Species
erysipelothrix
species: erysipelothrix rhusiopathiae and erysipelothrix tonsillarum
Taxonomy of the
Genus Erysipelothrix
Virulence Factors
of E. rhusiopathiae
Clinical
Significance of E. rhusiopathiae
Isolation and
Identification of E. rhusiopathiae
Antimicrobial
Susceptibility of E. rhusiopathiae
bacillus species
and related genera
Taxonomy and the
Taxonomic Dissection of the Genus Bacillus
Bacillus anthracis
Epidemiology of Anthrax
Virulence
Factors of B. anthracis
Clinical
Presentations of Anthrax
Treatment
of Anthrax
Prevention
of Anthrax
Bacillus cereus
Virulence
Factors of B. cereus
B.
cereus Gastroenteritis
Opportunistic
Bacillus Species Infections
Bacteremia
and Endocarditis
Infections
in Compromised Hosts
Ocular
Infections
Musculoskeletal
Infections
Nosocomial
Infections
Laboratory Safety,
Specimen Collection, and Processing
Isolation and
Identification of Bacillus Species: The “Bacillus cereus Group”; B. anthraxis,
B. cereus, B. thuringiensis, and B. mycoides
Antimicrobial
Susceptibility of Bacillus Species
corynebacterium
species
Introduction and
Taxonomy
Identification of
Corynebacterium Species and the Coryneform Bacteria
Antimicrobial
mSusceptibility Testing of Corynebacterium Species and
the Coryneform Bacteria
Members of the
Genus Corynebacterium Isolated From Humans
Corynebacterium amycolatum
Corynebacterium
diphtheriae
Corynebacterium
jeikeium
Corynebacterium
pseudodiphtheriticum
Corynebacterium
striatum
Corynebacterium urealyticum
Corynebacterium
Species Associated With Animals
Corynebacterium
Species Isolated From Foods and the Environment
other coryneform
bacteria
Actinobaculum
Species
Actinomyces
Species Isolated From Humans
Actinomyces
Species Isolated From Animals
Arcanobacterium
Species
Arthrobacter
Species
Brevibacterium
Species
Cellulomonas,
Cellullosimicrobium, and Oerskovia Species
Dermabacter
Species
Exiguobacterium
Species
Leifsonia
Species
Microbacterium
(Aureobacterium) Species
Rothia
and “Rothia-Like” Species (CDC Group 4)
Turicella
Species
gardnerella
vaginalis
Taxonomy
and Cellular Morphology
Virulence
Factors of G. vaginalis
Clinical
Significance of G. vaginalis
Antimicrobial
Susceptibility
lactobacillus
species
Taxonomy
and Epidemiology
Clinical
Significance
Isolation
and Identification
Antimicrobial
Susceptibility
Chapter 15: Aerobic Actinomycetes
introduction,
classification, and taxonomy
the nocardioform
group
Nocardia
Epidemiology, Pathology, and Pathogenesis
Clinical
Disease
Rhodococcus
Epidemiology, Pathology,
and Pathogenesis
Clinical
Disease
Other Nocardioform
Bacteria
the maduromycetes
and thermomonosporas
Actinomadura
Epidemiology,
Pathology, and Pathogenesis
Clinical
Disease
Nocardiopsis
the streptomycetes
Streptomycetes
thermophilic
actinomycetes
miscellaneous
actinomycetes
Oerskovia
Dermatophilus
Tropheryma
whipplei
History
and Taxonomy
Ecology
Clinical
Disease and Pathology
laboratory diagnosis of infections caused by aerobic
actinomycetes
Primary Isolation
Differentiation
of Nocardia From Other Genera of Aerobic Actinomycetes
Identification
of Thermophilic Actinomycetes
Identification
of Tropheryma whipplei
In
Vitro Susceptibility of Nocardia and Related Bacteria to Antimicrobial Agents and
Therapy of Infections
Chapter 16: The Anaerobic Bacteria
realtionships of
bacteria to oxygen
Oxygen
Tolerance
Oxidation-Reduction
Potential
habitats
taxonomic classification and nomenclature
human infections
isolation of anaerobic bacteria
Selection
of Specimens for Culture
Collection
and Transport of Specimens
Anaerobic
Blood Culture (Summary of Guidelines for Traditional Broth and Instrumented
Systems)
Direct
Examination of Clinical Materials
Selection
and Use of Media
anaerobic systems
for the cultivation of anaerobic bacteria
Anaerobic
Jar Techniques
Use
of the Anaerobic Glove Box
The
Roll-Streak System
Anaerobic
Disposable Plastic Bags
Use
of the Anaerobic Holding Jar
incubation of
cultures
inspection and
subculture of colonies
aerotolerance
tests
preliminary
reporting of results
determination of
cultural and biochemical characteristics for differentiation of anaerobic
isolates
Presumptive
Identification
Use
of Differential Agar Media
Presumpto Plates
Antimicrobial
Susceptibility Plates
Characterization
of anaerobes Using Conventional Biochemical Tests in Large Tubes
Alternative
Procedures
The Nagler Test and the
Packaged
Microsystems
Commercial
Packaged Kits for Identification of Anaerobes After 4
Hours of Incubation
determination of
metabolic products by gas-liquid chromatography
Identification of
Volatile Fatty Acids
Analysis
of Nonvolatile Acids
Gas-Liquid
Chromatography Controls
identification of
anaerobic bacteria
Anaerobic
Gram-Negative Non-Spore-Forming Bacilli
Classification and
Nomenclature
Presumptive or
Preliminary Group Identification of Bacteroides, Prevotella, Porphyromonas, and
Fusobacterium
Identification
of the Anaerobic Cocci
Identification
of the Anaerobic Non-Spore-Forming Gram-Positive Bacilli
Propionibacterium
Species
Bifidobacterium Species
Lactobacillus Species
Actinomyces Species
Eubacterium Species
Mobiluncus
and Bacterial Vaginosis
Additional
Genera and Species of Anaerobic Non-Spore-Forming Gram-Positive Bacilli
Identification of
Clostridium Species
Histotoxic
Clostridia Involved in Clostridial Myonecrosis or Gas Gangrene
Miscallenous
Clostridia in Other Clinical Settings
Clostridium
difficile-Associated Intestinal Disease
Botulism
Tetanus
antimicrobial susceptibility testing of anaerobic
bacteria
Methods of
Antimicrobial Susceptibility Testing of Anaerobes
Chapter 17: Antimicrobial Susceptibility Testing
historical
introduction
bacterial
resistance to antimicrobial agents
Mechanistic
Variables
Mechanisms
of Resistance
Transport of
Antimicrobial Agents Across the Cell Wall and Cell
Membranes
Antibiotics Taht
Interfere With formation of Bacterial Cell Walls: The b-Lactam and Glycopeptide Antibiotics
Antimicrobial Agents
That Do Not Exert Their Effect on Cell Walls
Interactions Among Resistance Mechanisms
laboratory
guidance of antimicrobial therapy
tests for
determining inhibitory activity of antimicrobial agents
Identification
Choice
of Test
Selection
of Antimicrobial Agents
Standardization
Growth Medium
pH
Serum
Cation Concentration
Atmosphere
Temperature
Inoculum
Antimicrobial Agents
Quality Control
Quality Assurance
Interpretation
of Results
Selection
of Antimicrobial Agents to Be Reported
Macrodilution
Broth Susceptibility Test
Agar
Dilution Susceptibility Test
Disk
Diffusion Susceptibility Test
Development of a
Standardized Disk Diffusion Procedure
Interpretation of
Results
Quality Control
Limitations
Microbroth
Dilution Susceptibility Test
Commercial
Systems
Vitek (BioMérieuxvitek,
Epsilomenter
Test (Etest; AB Biodisk, Sweden)
special issues in
susceptibility testing
b-Lactamases
Staphylococcus Species
Haemophilus Species
Neisseria gonorrhoeae
Moraxella (Branhamella)
catarrhalis
Enterococcus Species
Extended-Spectrum b-Lactamases
Staphylococcus
Species
b-Lactam Antibiotics (Oxacilling-Resistant
Staphylococcus Species)
Vancomycin
Macrolides,
Lincosamiedes, and Streptogramins
Fluoroquinolones
Haemophilus
Species
Penicillin Antibiotics
Chloramphenicol
Cephalosporins
Trimethoprim-Sulfamethoxazole
Streptococcus
pneumoniae
Penicillin
and Other b-Lactam Antibiotics
Multiple Resistance
Macrolides
and Lincosamides
Neisseria
gonorrhoeae
Neisseria
meningitidis
Enterococcus
Species
Aminoglycoside
Antibiotics
b-Lactam Antibiotics
Vancomycin
Listeria
monocytogenes
Streptococcus
pyogenes (Group A b-Hemolytic Streptococcus)
Penicillin
Erythromycin
Fluoroquinolones
Streptococcus
agalactiae (Group B b-Hemolytic
Streptococcus)
Viridans
Streptococci
Other
Gram-Positive Bacteria
Pseudomonas
aeruginosa, Burkholderia cepacia, and Stenotrophomonas maltophilia in Patients With Cystic Fibrosis
Direct
Susceptibility Testing
Chapter 18: Mycoplasmas and Ureaplasmas
taxonomy of
mycoplasmas and ureaplasmas
virulence factors
of human mycoplasmas
clinical
significance of the human mycoplasmas
Mycoplasma pneumoniae
Mycoplasma
hominis and Ureaplasma urealyticum
Mycoplasma
genitalium
Mycoplasma
fermentans
Mycoplasma
penetrans
Mycoplasma
pirum
Mycoplasma
primatum
Mycoplasma
spermatophilum
Human
Infections Due to Mycoplasma Species of Animal Origin
Hemotrophic
Mycoplasma Species
culture of human
mycoplasmas from clinical specimens
General
Considerations
Specimen
Collection
Transport
Media
Media
for Culture of Mycoplasmas
Isolation
and Identification of Mycoplasma pneumoniae
Noncultural
Detection of Mycoplasma pneumoniae
Isolation
and Identification of the Genital Mycoplasmas
Noncultural
Detection of the Genital Mycoplasmas
Commercial
Mycoplasma Culture Systems
Isolation
of Mycoplasmas on Routine Culture Media
serologic tests
for diagnosis of mycoplasma pneumoniae infections
serologic tests
for genital mycoplasmas
antimicrobial
susceptibility and treatment of mycoplasma infections
diagnosis and
treatment of hemotrophic mycoplasma infections in animals
trends in clinical
tuberculosis
Worldwide
Increase in the Incidence of Tuberculosis
Impact
of Coinfection With HIV and Mycobacterium tuberculosis
Personsl
at Risk for Tuberculosis
Rapidly
Progressive Disease
Implementation
of More Aggressive Infection Control and Epidemiologic Measures
trends in the
laboratory diagnosis of tuberculosis
Use
of Molecular Techniques
Use
of Automated Instruments
Use
of Broth Culture Media
Inoculation
of Clinical Specimens to Agar-Based Culture Media
Use
of p-nitro-acetylamino-hydroxypropiophenone (NAP)
Applications
of Gas-Liquid Chromatography, High-Performance Liquid Chromatography, and Mass
Spectrometry
Use
of the Lysis-Centrifugation System Blood Culture Tube
the clinical
laboratory
Optimizing
the Detection and Identification of Mycobacteria
Laboratory
Safety
specimen
collection
Respiratory
Specimens
Blood
Cultures
Stool
Specimens
Miscellaneous
“Sterile” Specimens
laboratory
approach to the recovery and identification of mycobacteria
Specimen
Preparation
Digestion
and Decontamination
Centrifugation
Bone
Marrow and Biopsy Specimens
Miscellaneous
Liquid Specimens
Staining
of Acid-Fast Bacilli
culture of
specimens for recovery of mycobacteria
Culture
Media
Nonselective
Culture Media for Recovery of Mycobacteria
Media
of Cohen and Middlebrock
Selective
Media
Incubation
rapid methods for
establishing a diagnosis
Sensitivity
of Acid-Fast Smears
Gas-Liquid
and High-Performance Liquid Chromatography
Use
of Broth Culture Medium
automated
detection systems
BACTEC
AFB System
Mycobacteria
Growth Indicator Tube (MGIT) and MGIT 960
MB/BacT
Mycobacteria Detection System
The
ESP Culture System II
The
BACTEC MYCO/F Lytic
manual detection systems
Septi-Chek
AFB System
idenfication of
mycobacteria using conventional methods
Optimal
Temperature for Isolation and Rates of Growth
Pigment Production
Niacin
Accumulation
Reduction of
Nitrates to Nitrites
Tween 80
Hydrolysis
Catalase Activity
Arylsulfatase
Activity
Urease Activity
Pyrazinamidase
Iron Uptake
Growth Inhibition
by Thiophene-2-carboxylic Acid Hydrazide
Growth in 5 %
Sodium Chloride
Growth on
MacConkey Agar
classification of mycobacteria
Laboratory
Identification of
Mycobacteria and Realted Clinical Syndromes
Review
of Mycobacterium Species: Laboratory Aspects and Clinical Correlations
Mycobacterium tuberculosis Complex
Photochromogens
Scotochromogens
Nonphotochromogens
Rapid
Growers
Other
Mycobacteria
The detection and identification
of mycobacteria by molecular methods
Signal-Amplification
Methods
Nucleic-Acid
Probes
In
Situ Hybridization
Nucleic-Acid
Amplification Methods
Commercially
Available Applications
Home-Brew
PCR Assays, Including Real-Time PCR
Postamplification
Analysis
Reverse
Hybridization
DNA
Sequencing
Microarray
Analysis
Strain Typing and
DNA Fingerprinting
susceptibility testing
short-course
therapy
American Thoracic
Society Recommendations
summary
Chapter 20:
Spirochetal Infections
taxonomy
treponema
Treponema pallidum
Subspecies pallidum
Incubation Period
Primary
Syphilis
Secondary
Syphilis
Latent
Syphilis
Epidemiology
Immunity
Treponema pallidum Subspecies pertenue
Treponema
pallidum Subspecies endemicum
Treponema
carateum
Laboratoy Diagnosis of Treponemal
Infections
Serologic
Tests
Innovations:
Provisional and Investigative Tests
borella
Relapsing
Fever
Epidemiology
Clinical
Disease
Laboratory
Diagnosis
Lyme Disease
Epidemiology
Clinical Disease
Laboratory Diagnosis
leptospira
Leptospirosis
Epidemiology
Clinical
Disease
Laboratory
Diagnosis
spirillum minor
(rat-bite Fever)
Chapter 21:
Mycology
patients at risk
for fungal infections
eneral Signs and Symptoms Suggesting Fungal
Infection
clinical
categorization of fungal infections
Common Mycologic
Terms
laboratory
approach to the diagnosis of fungal infections
pecimen Collection and Transport
Specimen
Processing
Direct
Examination
Preparation of Mounts for Study
Selection and
Inoculation of Culture Media
Incubation of Fungal
Cultures
laboratory
approach to the presumptive identification of fungal isolates
Extent of
Laboratory Genus/Species Identification
Genus
and Species Identification of the Major Groups of Fungi
Zygomyces Species and
Zygomycosis
Histopathology of
Infections Caused by the Zygomycetes
hyaline molds and
hyalohyphomycosis
Aspergillus
Species and Aspergillosis
Laboratory Presentation
Colony Morphology
Microscopic
Features
Aspergillus fumigatus
Aspergillus flavus
Aspergillus niger
Aspergillus terreus
Aspergillus nidulans
Histopathology
Diagnosis Using
Nonculture Techniques
Additional Rapidly
Growing Hyaline Molds
Colony Characteristics
Genera of Hyaline
Filamentous Molds Producing Conidia in Chains
Penicillium Species
Paeciliomyces Species
Scopulariopsis Species
Identification of
Hyaline Molds Producing Conidia in Clusters
Acremonium Species
Fusarium Species
Gliocladium Species
Trichoderma Species
Identification of
the Genera of Hyalohyphomycetes Producing Conidia Singly
Scedosporium Species
Chrysosporium Species
Sepedonium Species
Beauveria Species
identification of
the dermatophytes
Identification of
Microsporum Species
Microsporum canis
Microsporum gypseum
Microsporum nanum
Identification of
Trichophyton Species
Trichophyton mentagrophytes
Trichophyton tonsurans
Trichophyton verrucosum
Trichophyton floccosum
Diagnosis by
Nonculture Techniques
the dimorphic fungi
Blastomyces
dermatitidis and Blastomycosis
Laboratory Presentation
Diagnosis Using
Nonculture Techniques
Coccidioides
immitis and Coccidioidomycosis
Laboratory Presentation
Histoplasma
capsulatum and Histoplasmosis
Laboratory Presentation
Diagnosis Using
Nonculture Techniques
Sporothrix
schneckii and Sporotrichosis
Laboratory
Presentation
Diagnosis Using
Nonculture Techniques
Paracoccidioides
immitis and Paracoccidioidomycosis
Laboratory Presentation
Diagnosis Using
Nonculture Techniques
dematiaceous fungi
Agents of
Phaeohyphomycosis
Laboratory Presentation
Macroconidia With Transverse and Longitudinal Septa (Muriform)
Alternaria Species
Ulocladium Species
Stemphylium Species
Epicoccum Species
Macroconidia With Transverse Septa
Bipolaris Species
Drechslera Species
Curvularia Species
Exserohilum Species
Macroconidia Borne
Singly or Via Special Conidiation
Nigrospora Species
Phoma Species
Chaetomium Species
agents of
chromomycosis and mycetoma
Cladophialophora
(Cladosporium) carrionii
Phialophora
verrucosum
Phialophora
richardsiae
Fonsecaea
pedrosoi
Exophiala
jeanselmei
the laboratory
identification of yeasts
Germ Tube
Cornmeal
Agar Preparations
Growth
Patterns of Yeasts on Cornmeal Agar
CHROMagar
Candida
albicans
Candida
tropicalis
Candida
parapsilosis
Candida kefyr (pseudotropicalis)
Other
Emerging Pathogenic Candida Species
Candida
Species and Candidiasis
Species That
Produce True Hyphae
Species That Fail to
Produce True Hyphae
Cryptococcosis
and Cryptococcus neoformans
Diagnosis
by Nonculture Methods
Miscellaneous
Non-Hyphae-Forming Yeasts of Medical Importance
Candida
(Torulopsis) glabrata
Rhodotorula
Species
Saccharomyces
Species
Hansenula
anomala
Malassezia
furfur
Laboratory
Identification of “Black Yeasts”
Aureobasidium
pullulans
Phaeoannellomyces
werneckii
Packaged
Yeast-Identification Systems
Antifungal
Susceptibility Testing
serologic diagnosis of fungal diseases
Chapter 22:
Parasitology
risk and
prevention of parasitic infections
clinical
manifestations of parasitic disease
collection,
Transport, and processing of specimens
Fecal Specimens
Preservation of Clinical
Specimens
Visual Examination
Processing Fresh Stoohl Specimens
for Ova and Parasite Examination
Examination of
Intestinal Specimens Other Than Stool
Examination
of Extraintestinal Specimens
Sputum
Urine and Body Fluids
Tissue Biopsies and
Aspirates
Corneal Scrapings or
Biopsy
Muscle Biopsy
Blood
identification and
differentiation of parasites
Life Cycles of
Human Parasites
intestinal
protozoa
The Intestinal
Amoebae
Amebiasis and Entamoeba
histolytica
Entamoeba histolytica
versus Entamoeba coli
Serologic Diagnosis of
Amebiasis
Nonpathogenic Entamoeba
histolytica: Entamoeba dispar
Other Intestinal Amoebae
Protozoa
of Uncertain Classification
Intestinal
Flagellates
Giardia
lamblia
Other
Intestinal Flagellates
Ciliates:
Balantidium coli
Coccidia
Cryptosporidium
parvum
Cyclospora
cayetanensis
Isospora
belli
Sarcocystis
Species
Phylum
Microsporum: Microsporidium Species
nematodes
Ascariasis and
Ascaris lumbriocoides
Trichuriasis
and Trichuris trichiura (Whipworm)
Enterobius
vermicularis
Hookworms
Strongyloidiasis
and Strongyloides stercoralis
Trichostrongylus
Species
Capillaria
philippinensis
cestodes
Taenia
solium and Taenia saginata
Diphyllobothrium
latum: The Giant Fish Tapeworm
Hymenolepis
Species
Dipylidium
caninum
trematodes
Schistosomes
Fasciola
hepatica and Fasciolopsis buski
Clonorchis
sinensis
Paragonimus
westermani
blood and tissue
parasites
Malaria
Babesia
Hemoflagellates:
Leishmania Species and Trypanosoma Species
Leishmaniasis and Leishmania Species
Trypanosomiasis
Filarial Nematodes
and Filariasis
Onchocerciasis
and Onchocerca volvulus
Dracunculiasis
Dirofilariasis
Tissue Protozoan
Infections
Toxoplasma
gondii
Pneumocystis
carinii
Miscellaneous
Larval Tissue Parasite Infections
Trchinosis
Visceral
Larval Migrans
Cutaneous
Larva Migrans – Toxocara
Anisakiasis
Gnathostomiasis
Angiostrongyliasis
Echinococcosis
(Hydatid Disease)
Multiceps
Species – Coenurosis
Sparganosis:
Spirometra mansonoides
serologic
diagnosis of parasitic infections
drugs commonly
used in the treatment of parasitic diseases
Chapter 23:
Diagnosis of Infections Caused by Viruses, Chlamydia, Rickettsia, and Related
Organisms
introduction
Historical Review
Evolution
of Cell-Culture Techniques
Evolution
of Diagnostic Virology Services
Levels
of Service
Taxonomy and nomenclature
clinical manifestations of
viral infections
Orthomyxoviruses
Paramyxoviruses
Parainfluenza Viruses
Mumps Virus
Measles Virus
Respiratory Syncytial
Virus
Other Paramyxoviruses
Picornaviruses
Rhabdoviruses
Arenaviruses
Filoviruses
Togaviruses
Bunyaviruses
Hantaviruses
Human
Gastroenteritis Viruses
Rotaviruses
Caliciviruses
Astroviruses
Enteric Adenoviruses
Coronaviruses
Coltiviruses
Retroviruses
Herpesviruses
Herpes Simplex Virus
Cytomegalovirus
Epstein-Barr
Virus
Varicella-Zoster Virus
Human Herpesviruses-6
and –7
Human Herpesvirus-8
B-Virus
Adenoviruses
Poxviruses
Papovaviruses
Papillomaviruses
Polyomaviruses
Parvoviruses
Hepatitis
Viruses
Hepatitis A Virus
Hepatitis B Virus
Hepatitis C Virus
Hepatitis D Virus
Hepatitis E Virus
Prion Diseases
(Transmissible Spongiform Encephalopathies)
clinical
classification of viral infections
diagnosis of viral
infections
Collection of Specimens for Diagnosis
Transportation
and Sotrage of Specimens
Isolation
of Viruses in Culture
Preparation
and Maintenance of Cell Cultures
Contamination
of Cell Cultures
Technical
Aspects of Cell Culture
Selection
of Cell Cultures for Isolation of Viruses
Inoculation
and Incubation of Cell Cultures
Detection
of Virus and Provisional Identification
Cytopathic Effect
Hemagglutination and
Hemadsorption
Light Microscopy
Electron
Microscopy
Biochemical
Differentiation
Cell
Association
Detection
of Viral Antigens
Artifacts
and Non-Virus-Induced Changes
Definitive
Identification of Isolates
Storage of Viral
Isolates
Summary of
Detection and Identification of Viruses in Culture
direct detection
of viruses in clinical specimens
Light Microscopic
Detection of Inclusions
Electron
Microscopic Detection of Viral Particles
Immunologic
Detection of Viral Antigen
Respiratory Viruses
Herpes
Group Viruses
Other
Viruses
Molecular
Techniques
Human Immunodeficiency Virus
Hepatitis
C Virus
Hepatitis
B Virus
Human
Papillomaviruses
Parvovirus
B19
Herpes
Simplex Virus
Cytomegalovirus
Enteroviruses
SARS
Coronavirus
Other
Viral Infections
Selection of Tests
for Rapid Diagnosis
serologic diagnosis of viral infections
Human
Immunodeficiency Virus
Hepatitis
B Virus and Epstein-Barr Virus
Hepatitis
AVirus
Hepatitis
C Virus
Parvovirus
Herpes
Simplex Virus
Varicella-Zoster
Virus
Cytomegalovirus
Rubella
SARS
Coronavirus
Anti-IgM
Antibodies
Miscellaneous
Serologic Procedures
Antiviral
Susceptibility Testing
infections with
chlamydia species
Chlamydia
trachomatis
Clinical Features and Epidemiology
Collection of Specimens
Isolation of Chlamydia trachomatis
in Clinical Specimens
Direct Detection of
Chlamydia trachomatis in Clinical Specimens
Serologic Diagnosis
Other Methods for
Diagnosis
Diagnosis for Sexual
Abuse
Chlamydia
psittaci
Chlamydia
pneumoniae
infections with
rickettsia, coxiella, ehrlichia, and anaplasma
Rickettsia
and Coxiella
Clinical Features and Epidemiology
Collection of Specimens
Isolation of Rickettsia
and Coxiella in Culture
Direct Detection of
Antigen and Nucleic Acid in Clinical Specimens
Serologic Diagnosis
Ehrlichia and
Anaplasma Species
Appendix I
Appendix II
Chart
1-1 Catalase
Chart
1-2 Bile-Solubility Test
Chart
1-3 The
Slide Coagulase Test
Chart
1-4 Indole Test
Chart
1-5 Cytochrome Oxidase Test
Chart
1-6 PYR Test
Chart
3-1 Complement Fixation (CF)
Test
Chart
3-2 Hemagglutination
Inhibition (HAI) Test
Chart
6-1 o-Nitrophenyl-b-D-Galactopyranoside
Chart
6-2 Nitrate Reduction: General
Applications
Chart
6-3 Methyl Red
Chart
6-4 Voges-Proskauer Test
Chart
6-5 Citrate Utilization
Chart
6-6 Urease: Conventional
Chart
6-7 Decarboxylases
Chart
6-8 Phenyalalanine Deaminase
Chart
7-1 Oxidative-Fermentative
Test (Hugh and Leifson)
Chart
7-2 Flagellar Stain
Chart
7-3 Fluorescence-Denetrification
Chart
7-4 Esculin Hydrolysis Test
Chart
8-1 The
Chart
9-1 Test for X and V Factor
Requirements
Chart
11-1 Rapid Carbohydrate
Utilization Test for Identification of Neisseria Species
Chart
12-1 Furazolidone Disk Test
Chart
13-1 Novobiocin Disk Test
Chart
13-2 Bile-Esculin-Test
Chart
13-3 Optochin Susceptibility Test
Chart
13-4 Salt-Tolerance Test
Chart
14-1 Loefflers` Methylene Blue
Stain
Chart
14-2 Loefflers` Serum Medium
Chart
14-3 Tinsdales` Agar (as Modified
by Moore and Parsons)
Chart
14-4 Cystine-Tellurite Blood Agar
Chart
15-1 Hydrolysis of Xanthine,
Hypoxanthine, Tyrosine, and Casein
Chart
17-1 Disk Diffusion (Bauer-Kirby)
Susceptibility Test for Nonfastidious Bacteria
Chart
17-2 Performance of Microbroth
Dilution Susceptibility tests with Nonfastidious Bacteria
Chart
17-3 Gradient Diffusion Test
(Etest) for Bacterial Susceptibility
Chart
18-1 Diene`s Stain Procedure for
Identification of Mycoplasmas
Chart
18-2 Hemadsorption Test for
Identification of Mycoplasma pneumoniae
Chart
18-3 Manganous Chloride-Urea Test
for Identification of Ureaplasma urealyticum
Chart
18-4 Medium for Isolation of
Mycoplasma pneumoniae
Chart
18-5 Medium for Isolation of
Genital Mycoplasmas
Chart
18-6 Tetrazolium Reduction Test
for the Presumptive Identification of Mycoplasma pneumoniae
Chart
19-1 Digestion and
Decontamination: N-Acetyl-L-cysteine-Sodium Hydroxide (NALC)
Chart
19-2 Carbol Fuchsin Stains
Chart 19-3 Fluorescent Stain: Auramine 0; Auramine-Rhodamine
Chart
19-4 NAP Test (p-Nitro-a-Acetylamino-b-Hydroxypropiophenone);
(BACTEC)
Chart
19-5 Arylsulfatase
Chart
19-6 Assessment of
Photoreactivity of Mycobacteria
Chart
19-7 Catalase 68°C
Chart
19-8 Growth on MacConkey Agar
Chart
19-9 Inhibition by
Thiopene-2-carboxylic Acid Hydrazide (T2H, 1µg/mL)
Chart
19-10 Iron Uptake
Chart
19-11 Niacin Accumulation
Chart
19-12 Nitrate Reduction:
Mycobacteria
Chart
19-13 Parazinamidase
Chart
19-14 Sodium Chloride Tolerance:
Mycobacteria
Chart
19-15 Twee-80 Hydrolysis
Chart
19-16 Urease: Mycobacteria
Chart
19-17 DNA Probes for the
Identification of Mycobacteria
Chart
19-18 Detection, Identification,
and Drug Susceptibility Testing of M. tuberculosis by Radiometric
Instrumentation
Chart
20-1 Darfield Microscopy of
Genital Lesions
Chart
20-2 Venereal Disease Research
Laboratory (VDRL) Slide Test on Serum
Chart
20-3 Rapid Plasma Reagin (RPR)
Card Test
Chart
20-4 Fluorescent Treponemal
Antibody Absorption Test (FTA-ABS)
Chart 22-1 Fecal Concentration Techniques for the Recovery of
Intestinal Parasites
Chart
22-2 Trichrome-Staining Technique
for Fecal Smears
Chart
22-3 Preparation of Thin and
Thick Blood Smears
Chart
22-4 Calibration of the Ocular
Micrometer
Chart
22-5 Cellulose Tape Preparation
for Pinworm Examination
Chart
23-1 Hemadsorption (HAD) Test
Chart
A-1 Formulations of Commonly
Used Stool Preservatives
Color
Plates
Index