Bailey & Scott’s Diagnostic Microbiology

Description

Cover Page Front matter Bailey & scott’s diagnostic microbiology Copyright Dedication Reviewers Contributors Preface Acknowledgments Table of contents Part I Basic Medical Microbiology 1 Microbial taxonomy Objectives Classification Family Genus Species Nomenclature Identification Identification methods Bibliography 2 Bacterial genetics, metabolism, and structure Objectives Bacterial genetics Nucleic acid structure and organization Nucleotide structure and sequence DNA molecular structure Genes and the genetic code Chromosomes Nonchromosomal elements Replication and expression of genetic information Replication Expression of genetic information Transcription Translation Regulation and control of gene expression Genetic exchange and diversity Mutation Genetic recombination Genetic exchange Transformation. Transduction Conjugation Bacterial metabolism Fueling Acquisition of nutrients Production of precursor metabolites Energy production Oxidative phosphorylation Biosynthesis Polymerization and assembly Structure and function of the bacterial cell Eukaryotic and prokaryotic cells Bacterial morphology Bacterial cell components Cell envelope Outer membrane Cell wall (murein layer) Periplasmic space Cytoplasmic (inner) membrane Cellular appendages Cell interior Bibliography 3 Host-microorganism interactions Objectives The encounter between host and microorganism The human host’s perspective Microbial reservoirs and transmission Human and microbe interactions Animals as microbial reservoirs Insects as vectors The environment as a microbial reservoir The microorganism’s perspective Microorganism colonization of host surfaces The host’s perspective Skin and skin structures Mucous membranes General protective characteristics Specific protective characteristics The microorganism’s perspective Microbial colonization Microorganism entry, invasion, and dissemination The host’s perspective Disruption of surface barriers Responses to microbial invasion of deeper tissues Nonspecific responses Phagocytes Inflammation Specific responses—the immune system Components of the immune system Two branches of the immune system The microorganism’s perspective Colonization and infection Pathogens and virulence Microbial virulence factors Attachment Invasion. Survival against inflammation Survival against the immune system Microbial toxins Genetics of virulence: Pathogenicity islands Biofilm formation Outcome and prevention of infectious diseases Outcome of infectious diseases Prevention of infectious diseases Immunization Epidemiology Bibliography Part II General Principles in Clinical Microbiology Section 1 Safety and Specimen Management 4 Laboratory safety Objectives Sterilization, disinfection, and decontamination Methods of sterilization Methods of disinfection Physical methods of disinfection Chemical methods of disinfection Antiseptics Chemical safety Fire safety Electrical safety Handling of compressed gases Biosafety Exposure control plan Employee education and orientation Disposal of hazardous waste Standard precautions Engineering controls Laboratory environment Biologic safety cabinet Personal protective equipment Postexposure control Classification of biologic agents based on hazard Mailing biohazardous materials Bibliography 5 Specimen management Objectives General concepts for specimen collection and handling Appropriate collection techniques Specimen transport Specimen preservation Specimen storage Specimen labeling Specimen requisition Rejection of unacceptable specimens Specimen processing Gross examination of specimen Direct microscopic examination Selection of culture media Specimen preparation Inoculation on solid media Incubation conditions Specimen workup Extent of identification required Communication of laboratory findings Critical (panic) values Expediting results reporting: Computerization Bibliography Section 2 Approaches to Diagnosis of Infectious Diseases 6 Role of microscopy Objectives Bright-field (light) microscopy Principles of light microscopy Magnification Resolution Contrast Direct and indirect smears Staining techniques Gram stain Procedure overview Principle Gram stain examination (direct smear) Gram stain of bacteria grown in culture (indirect smear) Acid-fast stains Principle Procedure overview Phase-contrast microscopy Fluorescent microscopy Principle of fluorescent microscopy Staining techniques for fluorescent microscopy Fluorochroming Acridine orange Auramine-rhodamine Calcofluor white Immunofluorescence Dark-field microscopy Electron microscopy Digital automated microscopy Bibliography 7 Traditional cultivation and identification Objectives Organism identification Principles of bacterial cultivation Nutritional requirements General concepts of culture media Phases of growth media Media classifications and functions Summary of artificial media for routine bacteriology Brain-heart infusion Chocolate agar Columbia cna with blood Gram-negative broth Hektoen enteric agar Macconkey agar Phenylethyl alcohol agar Sheep blood agar Modified thayer-martin agar Thioglycollate broth Xylose-lysine-deoxycholate agar Preparation of artificial media Media sterilization Cell cultures Environmental requirements Oxygen and carbon dioxide availability Temperature Ph Moisture Methods for providing optimal incubation conditions Bacterial cultivation Isolation of bacteria from specimens Evaluation of colony morphologies Type of media supporting bacterial growth Relative quantities of each colony type Colony characteristics Indirect gram stain and subcultures Principles of identification Organism identification using genotypic criteria Organism identification using phenotypic criteria Microscopic morphology and staining characteristics Macroscopic (colony) morphology Environmental requirements for growth Resistance or susceptibility to antimicrobial agents Nutritional requirements and metabolic capabilities Establishing enzymatic capabilities Types of enzyme-based tests Single enzyme tests Catalase test Oxidase test Indole test Urease test Pyr test Hippurate hydrolysis Tests for the presence of metabolic pathways Oxidation and fermentation tests Amino acid degradation Single substrate utilization Establishing inhibitor profiles Principles of phenotypic identification schemes Selection and inoculation of identification test battery Type of bacteria to be identified Clinical significance of the bacterial isolate Availability of reliable testing methods Incubation for substrate utilization Conventional identification Rapid identification Matrix-assisted laser desorption ionization time of flight mass spectrometry Detection of metabolic activity Colorimetry Fluorescence Turbidity Analysis of metabolic profiles Identification databases Use of the database to identify unknown isolates Confidence in identification Commercial identification systems and automation Advantages and examples of commercial system designs Overview of commercial identification systems Bibliography 8 Nucleic acidbased analytic methods for microbial identification and characterization Objectives Overview of nucleic acid–based methods Specimen collection and transport Nucleic acid hybridization methods Hybridization steps and components Production and labeling of probe nucleic acid Preparation of target nucleic acid Mixture and hybridization of target and probe Detection of hybridization Hybridization formats Liquid format Solid support format In situ hybridization Peptide nucleic acid fluorescence in situ hybridization Hybridization with signal amplification Amplification methods—polymerase chain reaction–based Overview of polymerase chain reaction and derivations Extraction and denaturation of the target nucleic acid Primer annealing Extension of the primer-target duplex Detection of polymerase chain reaction products Derivations of the polymerase chain reaction method Real-time polymerase chain reaction Amplification methods: Non–polymerase chain reaction–based Coupled target and signal (probe) amplification Isothermal (constant temperature) amplification Sequencing and enzymatic digestion of nucleic acids Nucleic acid sequencing Postamplification and traditional analysis Nucleic acid electrophoresis Pyrosequencing High-density deoxyribonucleic acid (DNA) probes Low- to moderate-density arrays Enzymatic digestion and electrophoresis of nucleic acids Applications of nucleic acid–based methods Direct detection of microorganisms Advantages and disadvantages Analytical specificity Analytical sensitivity Applications for direct molecular detection of microorganisms Identification of microorganisms grown in culture Characterization of microorganisms beyond identification Detection of antimicrobial resistance Investigation of strain relatedness and pulsed-field gel electrophoresis Automation and advances in molecular diagnostic instrumentation Bibliography 9 Overview of immunochemical methods used for organism detection Objectives Features of the immune response Characteristics of antibodies Features of the humoral immune response useful in diagnostic testing Interpretation of serologic tests Production of antibodies for use in laboratory testing Polyclonal antibodies Monoclonal antibodies Igm clinical significance Separating igm from igg for serologic testing Principles of immunochemical methods used for organism detection Precipitation tests Double immunodiffusion Single immunodiffusion Particle agglutination Coagglutination Hemagglutination Hemagglutination inhibition assays Flocculation tests Neutralization assays Complement fixation assays Immunofluorescent assays Enzyme immunoassays Solid-phase immunoassay Membrane-bound solid-phase enzyme immunosorbent assay Automated fluorescent immunoassays Western blot immunoassays Summary Bibliography Section 3 Evaluation of Antimicrobial Activity 10 Principles of antimicrobial action and resistance Objectives Antimicrobial action Principles Mode of action of antibacterial agents Inhibitors of cell wall synthesis Beta-lactams Fosfomycin Glycopeptides and lipoglycopeptides Inhibitors of cell membrane function Lipopeptides Inhibitors of protein synthesis Aminoglycosides Macrolide-lincosamide-streptogramin group Ketolides Oxazolidinones Chloramphenicol Tetracyclines Glycylglycines Inhibitors of deoxyribonucleic acid and ribonucleic acid synthesis Fluoroquinolones Metronidazole Rifamycin Inhibitors of other metabolic processes Sulfonamides Trimethoprim Nitrofurantoin Mechanisms of antibiotic resistance Principles Biologic versus clinical resistance Environmentally mediated antimicrobial resistance Microorganism-mediated antimicrobial resistance Intrinsic resistance Acquired resistance Common pathways for antimicrobial resistance Resistance to beta-lactam antibiotics Resistance to glycopeptides Resistance to aminoglycosides Resistance to quinolones Resistance to other antimicrobial agents Emergence and dissemination of antimicrobial resistance Bibliography 11 Laboratory methods and strategies for antimicrobial susceptibility testing Objectives Goal and limitations Standardization Limitations of standardization Testing methods Principles Methods that directly measure antimicrobial activity Conventional testing methods: General considerations Inoculum preparation Selection of antimicrobial agents for testing Conventional testing methods: Broth dilution Procedures Medium and antimicrobial agents. Inoculation and incubation. Reading and interpretation of results. Advantages and disadvantages. Conventional testing methods: Agar dilution Conventional testing methods: Disk diffusion Procedures Medium and antimicrobial agents. Inoculation and incubation. Reading and interpretation of results. Advantages and disadvantages. Commercial susceptibility testing systems Broth microdilution methods Agar dilution derivations Diffusion in agar derivations Automated antimicrobial susceptibility test systems Alternative approaches for enhancing resistance detection Supplemental testing methods Predictor antimicrobial agents Methods that directly detect specific resistance mechanisms Phenotypic methods Beta-lactamase detection Chloramphenicol acetyltransferase detection Genotypic methods Special methods for complex antimicrobial/organism interactions Bactericidal tests Minimal bactericidal concentration Time-kill studies Serum bactericidal test (schlichter test) Tests for activity of antimicrobial combinations Laboratory strategies for antimicrobial susceptibility testing Relevance When to perform a susceptibility test Determining clinical significance Predictability of antimicrobial susceptibility Availability of reliable susceptibility testing methods Selection of antimicrobial agents for testing Accuracy Use of accurate methodologies Review of results Components of results review strategies Data review Resolution Accuracy and antimicrobial resistance surveillance Communication Reference Bibliography Part III Bacteriology Section 1 Principles of Identification 12 Overview of bacterial identification methods and strategies Objectives Rationale for approaching organism identification Future trends of organism identification Bibliography Section 2 Catalase-Positive, Gram-Positive Cocci 13 and similar organisms Objectives General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Microscopy Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Comments regarding specific organisms Serodiagnosis Molecular methods Other identification methods Antimicrobial susceptibility testing and therapy Prevention Bibliography Section 3 Catalase-Negative, Gram-Positive Cocci 14 and similar organisms Objectives General characteristics Epidemiology Pathogenesis and spectrum of disease Beta-hemolytic streptococci Streptococcus pneumoniae Viridans streptococci Enterococcus species Miscellaneous other gram-positive cocci Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Antigen detection Molecular methods Gram stain Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Matrix-assisted laser desorption ionization time-of-flight mass spectrometry Comments regarding specific organisms Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography Section 4 Non-Branching, Catalase-Positive, Gram-Positive Bacilli 15 and similar organisms Objectives General characteristics Bacillus anthracis Epidemiology Pathogenesis and spectrum of disease B. cereus group (not b. anthracis) Epidemiology Pathogenesis and spectrum of disease B. thuringiensis B. subtilis, brevibacillus spp., and paenibacillus spp. Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Specimen processing Direct detection methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Serodiagnosis Molecular methods Antimicrobial susceptibility testing and therapy Prevention Bibliography 16 and similar organisms Objectives General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Matrix-assisted laser desorption ionization time-of-flight mass spectrometry Molecular methods Comments on specific organisms Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Treatment Bibliography Section 5 Non-Branching, Catalase-Negative, Gram-Positive Bacilli 17 and similar organisms Objectives General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Cultivation Media of choice. Incubation conditions and duration Colonial appearance Approach to identification Matrix-assisted laser desorption ionization time-of-flight mass spectrometry Molecular methods Comments regarding specific organisms Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography Section 6 Branching or Partially Acid-Fast, Gram-Positive Bacilli 18 and similar organisms Objectives General characteristics Partially acid-fast aerobic actinomycetes Nocardia spp. Rhodococcus, dietzia, gordonia and tsukamurella spp. Non–acid-fast aerobic actinomycetes: streptomyces, actinomadura, dermatophilus, nocardiopsis, and the thermophilic actin ... Epidemiology and pathogenesis Partially acid-fast aerobic actinomycetes Nocardia spp. Rhodococcus, dietzia, gordonia, tsukamurella spp. Non–acid-fast aerobic actinomycetes: streptomyces, actinomadura, dermatophilus, nocardiopsis, and the thermophilic actin ... Spectrum of disease Partially acid-fast aerobic actinomycetes Nocardia spp. Rhodococcus, gordonia, tsukamurella spp. Non–acid-fast aerobic actinomycetes: streptomyces, actinomadura, dermatophilus, nocardiopsis, and the thermophilic actin ... Laboratory diagnosis Specimen collection, transport, and processing Direct detection methods Molecular methods Matrix-assisted laser desorption ionization time-of-flight mass spectrometry Cultivation Approach to identification Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography Section 7 Gram-Negative Bacilli and Coccobacilli (MacConkey-Positive, Oxidase-Negative) 19 Enterobacteriaceae Objectives General characteristics Epidemiology Pathogenesis and spectrum of diseases Specific organisms Opportunistic human pathogens Averyella dalhousiensis Citrobacter spp. Cronobacter spp. Edwardsiella tarda Enterobacter spp. Escherichia coli Ewingella americana Hafnia alvei Klebsiella spp. Morganella spp. Pantoea spp. Plesiomonas shigelloides Proteus spp. and providencia spp. Serratia spp. Primary intestinal pathogens Salmonella Shigella spp. Yersinia spp. Rare human pathogens Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Molecular methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Specific considerations for identifying enteric pathogens Serodiagnosis Matrix-assisted laser desorption ionization time-of-flight mass spectrometry Antimicrobial susceptibility testing and therapy Extended spectrum beta-lactamase–producing enterobacteriaceae Expanded-spectrum cephalosporin resistance and carbapenemase resistance Multidrug-resistant typhoid fever Prevention Bibliography 20 and other organisms Objectives General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Comments regarding specific organisms Serodiagnosis Antimicrobial resistance and antimicrobial susceptibility testing Antimicrobial therapy Prevention Bibliography Section 8 Gram-Negative Bacilli and Coccobacilli (MacConkey-Positive, Oxidase- Positive) 21 and similar organisms Objectives General characteristics Epidemiology Burkholderia spp. and ralstonia spp. Pseudomonas spp. and brevundimonas spp. Pathogenesis and spectrum of disease Burkholderia spp. and ralstonia spp. Pseudomonas spp. and brevundimonas spp. Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Molecular methods Additional detection methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Comments regarding specific organisms Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography 22 and similar organisms Objectives General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Comments regarding specific organisms Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography 23 and similar organisms Objectives General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Comments regarding specific organisms Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography 24 (nonpertussis), and similar organisms Objectives General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Comments regarding specific organisms Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography 25 and similar organisms Objectives General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Comments regarding specific organisms Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography Section 9 Gram-Negative Bacilli and Coccobacilli (MacConkey-Negative, Oxidase-Positive) 26 and similar organisms Objectives General considerations Epidemiology, spectrum of disease, and antimicrobial therapy Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Comments regarding specific organisms Acidovorax facilis Cdc groups iic, iie, iih, III, o-1, o-2, and o-3 Sphingobacterium mizutaii Sphingobacterium multivorum Sphingobacterium spiritivorum Sphingomonas paucimobilis Sphingomonas parapaucimobilis Antimicrobial susceptibility Serodiagnosis Prevention Bibliography 27 Moraxella Objectives General characteristics Epidemiology, spectrum of disease, and antimicrobial therapy Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Comments regarding specific organisms Serodiagnosis Prevention Bibliography 28 and similar organisms Objectives General characteristics Epidemiology, spectrum of disease, and antimicrobial therapy Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Comments regarding specific organisms Serodiagnosis Prevention Bibliography 29 and similar organisms Objectives General characteristics and taxonomy Epidemiology, spectrum of disease, and antimicrobial therapy Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Comments regarding specific organisms Serodiagnosis Prevention Bibliography 30 and similar organisms Objectives General characteristics Epidemiology, pathogenesis, and spectrum of disease and antimicrobial therapy Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Comments regarding specific organisms Serodiagnosis Prevention Bibliography Section 10 Gram-Negative Bacilli and Coccobacilli (MacConkey-Negative, Oxidase- Variable) 31 Haemophilus Objectives General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Direct observation Antigen detection Molecular methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Serotyping Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography Section 11 Gram-Negative Bacilli that are Optimally Recovered on Special Media 32 Bartonella and Afipia Objectives Bartonella General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Specimen collection, transport, and processing Direct detection methods Cultivation Approach to identification Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Afipia felis Bibliography 33 Campylobacter, Arcobacter, and Helicobacter Objectives Campylobacter and arcobacter General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Specimen collection, transport, and processing Direct detection Antigen detection Media Cultivation Stool Blood Atmosphere Approach to identification Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Helicobacter spp. General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Specimen collection, transport, and processing Direct detection Cultivation Approach to identification Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography 34 Legionella Objectives General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Stains Antigens Molecular methods Cultivation Approach to identification Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography 35 Brucella Objectives General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Specimen collection, transport, and processing Direct detection methods Cultivation Approach to identification Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography 36 and related species Objectives General characteristics Epidemiology and pathogenesis Pathogenesis Spectrum of disease Laboratory diagnosis Specimen collection, transport, and processing Direct detection methods Cultivation Approach to identification Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography 37 Francisella Objectives General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Specimen collection, transport, and processing Direct detection methods Cultivation Approach to identification Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography 38 Streptobacillus moniliformis and Spirillum minus Objectives Streptobacillus moniliformis General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Specimen collection, transport, and processing Direct detection methods Cultivation Approach to identification Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Spirillum minus General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Specimen collection, transport, and processing Direction detection methods Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Bibliography Section 12 Gram-Negative Cocci 39 Neisseria and Moraxella catarrhalis Objectives General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Gram stain Molecular methods Cultivation Media of choice Incubation conditions and duration Colonial appearance Approach to identification Biochemical identification Comments about specific organisms Immunoserologic identification Serotyping Antimicrobial susceptibility testing and therapy Prevention Bibliography Section 13 Anaerobic Bacteriology 40 Overview and general laboratory considerations Objectives General characteristics Specimen collection and transport Macroscopic examination of specimens Direct detection methods Antigen detection Gram staining Specimen processing Anaerobe jars or pouches Holding jars Anaerobe chamber Anaerobic media Incubation conditions and duration Approach to identification Examination of primary plates Subculture of isolates Presumptive identification of isolates Definitive biochemical identification Rapid identification methods Antimicrobial susceptibility testing and therapy Bibliography 41 Overview of anaerobic organisms Objectives Epidemiology Pathogenesis and spectrum of disease Gram-positive, spore-forming bacilli Laboratory diagnosis and specimen collection Gram-positive, non–spore-forming bacilli Laboratory diagnosis Gram-negative rods Bacteroides fragilis group Nonpigmented prevotella spp. Pigmented porphyromonas and prevotella spp. Fusobacteriaceae Proteobacteria Anaerobic gram-positive and gram-negative cocci Laboratory diagnosis Result reporting Prevention Bibliography Section 14 Mycobacteria and Other Bacteria with Unusual Growth Requirements 42 Mycobacteria Objectives Mycobacterium tuberculosis complex General characteristics Epidemiology and pathogenesis Epidemiology Pathogenesis Spectrum of disease Nontuberculous mycobacteria Slow-growing nontuberculous mycobacteria Photochromogens Scotochromogens Nonphotochromogens Mycobacterium avium complex General characteristics. Epidemiology and pathogenesis. Clinical spectrum of disease. Other nonphotochromogens Rapidly growing nontuberculous mycobacteria General characteristics Epidemiology and pathogenesis Spectrum of disease Noncultivatable nontuberculous mycobacteria—mycobacterium leprae General characteristics Epidemiology and pathogenesis Epidemiology Pathogenesis Spectrum of disease Laboratory diagnosis of mycobacterial infections Specimen collection and transport Pulmonary specimens Gastric lavage specimens Urine specimens Fecal specimens Tissue and body fluid specimens Blood specimens Wounds, skin lesions, and aspirates Specimen processing Contaminated specimens Inadequate specimens and rejection criteria Overview Special considerations Specimens not requiring decontamination Direct detection methods Microscopy Acid-fast stains Methods Fluorochrome stain. Fuchsin acid-fast stains. Examination, interpretation, and reporting of smears Antigen-protein detection Immunodiagnostic testing Genetic sequencing and nucleic acid amplification DNA microarrays Matrix-assisted laser desorption ionization time-of-flight mass spectrometry Cultivation Solid media Liquid media Interpretation Approach to identification Conventional phenotypic tests Growth characteristics Growth rate. Pigment production. Biochemical testing Niacin. Nitrate reduction. Catalase. Tween 80 hydrolysis. Tellurite reduction. Arylsulfatase. Growth inhibition by thiophene-2-carboxylic acid hydrazide. Other tests. Antimicrobial susceptibility testing and therapy M. tuberculosis complex Direct versus indirect susceptibility testing Conventional methods Molecular methods for the determination of susceptibility Therapy Nontuberculous mycobacteria Prevention Bibliography 43 Obligate intracellular and nonculturable bacterial agents Objectives Chlamydia Chlamydia trachomatis General characteristics Epidemiology and pathogenesis Spectrum of disease Trachoma Lymphogranuloma venereum Oculogenital infections Perinatal infections Laboratory diagnosis Specimen collection and transport Cultivation Direct detection methods Cytologic examination. Antigen detection and nucleic acid hybridization. Nucleic acid amplification tests. Serodiagnosis Antibiotic susceptibility testing and therapy Prevention Chlamydia psittaci General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Antibiotic susceptibility testing and therapy Prevention Chlamydia pneumoniae General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Direct detection methods Cultivation Serodiagnosis Antibiotic susceptibility testing and therapy Prevention Rickettsia, orientia, anaplasma, and ehrlichia General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Direct detection methods Cultivation Serodiagnosis Antibiotic susceptibility testing and therapy Prevention Coxiella General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Antibiotic susceptibility testing and therapy Prevention Tropheryma whipplei General characteristics Epidemiology, pathogenesis, and spectrum of disease Laboratory diagnosis Antibiotic susceptibility testing and therapy Prevention Klebsiella granulomatis General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Antibiotic susceptibility testing and therapy Bibliography 44 Cell wall-deficient bacteria: and Objectives General characteristics Epidemiology and pathogenesis Epidemiology Pathogenesis Spectrum of disease Laboratory diagnosis Specimen collection, transport, and processing Direct detection methods Molecular methods Cultivation Approach to identification Serodiagnosis Susceptibility testing and therapy Prevention Bibliography 45 The spirochetes Objectives Treponema General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Specimen collection Direct detection Molecular methods Serodiagnosis Antimicrobial susceptibility testing and therapy Prevention Borrelia General characteristics Epidemiology and pathogenesis Relapsing fever Lyme disease Spectrum of disease Relapsing fever Lyme disease Laboratory diagnosis Specimen collection, transport, and processing Direct detection methods Relapsing fever Lyme disease Cultivation Serodiagnosis Relapsing fever Lyme disease Molecular methods Antibiotic susceptibility testing and therapy Prevention Brachyspira General characteristics Epidemiology and pathogenesis Laboratory diagnosis Specimen collection and direct detection Cultivation Approach to identification Antibiotic susceptibility and therapy Leptospira General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Specimen collection, transport, and processing Direct detection Cultivation Approach to identification Serodiagnosis Molecular methods Antibiotic susceptibility and therapy Prevention Bibliography Part IV Parasitology 46 Overview of the methods and strategies in parasitology Objectives Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Specimen collection and transport Specimen processing Approach to identification Microscopic examination Intestinal tract Ova and parasite examination Recovery of the tapeworm scolex Examination for pinworm Sigmoidoscopy material Duodenal drainage Duodenal capsule technique (entero-test) Urogenital tract specimens Sputum Aspirates Biopsy specimens Blood Thin blood films Thick blood films Buffy coat films Direct detection methods Intestinal parasites Blood parasites Cultivation Larval-stage nematodes Blood protozoa Serodiagnosis Prevention 47 Intestinal protozoa Objectives Amoebae Entamoeba histolytica General characteristics Epidemiology Pathogenesis and spectrum of disease Asymptomatic infection Intestinal disease Hepatic disease Metastatic amebiasis Laboratory diagnosis Routine methods Antigen detection Histology Molecular methods Antibody (serologic) detection Reporting of results Therapy Asymptomatic infection Prevention Entamoeba coli General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Entamoeba hartmanni General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Endolimax nana General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Iodamoeba bütschlii (buetschlii) General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention (E. hartmanni, E. nana, I. bütschlii) Blastocystis hominis General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Routine methods Antigen detection Antibody (serologic) detection Reporting of results Therapy Prevention Flagellates Giardia duodenalis General characteristics Epidemiology Pathogenesis and spectrum of disease Asymptomatic infection Intestinal disease Chronic disease Antigenic variation Laboratory diagnosis Routine methods Antigen detection Antibody detection Histology Molecular methods Results and reporting Prevention Treatment Chilomastix mesnili General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Dientamoeba fragilis General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Routine methods Antigen detection Antibody detection Therapy Prevention Pentatrichomonas hominis Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Ciliates Balantidium coli General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Results reporting Therapy Prevention Sporozoa (apicomplexa) Cryptosporidium spp. General characteristics Epidemiology Pathogenesis and spectrum of disease Immunocompetent individuals Immunocompromised individuals Laboratory diagnosis Routine methods Antigen detection Molecular methods Antibody detection Histology Results reporting Therapy Prevention Cyclospora cayetanensis General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Special stains Flow cytometry Molecular methods and other tests Results and reporting Therapy Prevention Cystoisospora belli General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Molecular methods Histology Results and reporting Therapy Prevention Sarcocystis spp. General characteristics Pathogenesis and spectrum of disease Laboratory diagnosis Molecular methods Results and reporting Therapy Prevention Microsporidia General characteristics Epidemiology Pathogenesis and spectrum of disease Enterocytozoon bieneusi Encephalitozoon spp. Encephalitozoon intestinalis Other microsporidia Laboratory diagnosis Antigen detection Antibody detection Molecular methods Histology Results and reporting Therapy Prevention Bibliography 48 Blood and tissue protozoa Objectives Plasmodium spp. Plasmodium vivax (benign tertian malaria) General characteristics Pathogenesis and spectrum of disease Plasmodium ovale General characteristics Pathogenesis and spectrum of disease Plasmodium malariae (quartan malaria) General characteristics Pathogenesis and spectrum of disease Plasmodium falciparum (malignant tertian malaria) General characteristics Pathogenesis and spectrum of disease Plasmodium knowlesi (simian malaria, the fifth human malaria) General characteristics Pathogenesis and spectrum of disease Laboratory diagnosis (all species) Routine methods Antigen-based tests Serologic tests Molecular methods Automated instruments Results reporting Therapy Babesia spp. General characteristics Organism Pathogenesis and spectrum of disease Laboratory diagnosis Routine methods Serologic tests Molecular methods Results reporting Therapy Prevention Trypanosoma spp. African trypanosomiasis General characteristics Pathogenesis and spectrum of disease Trypanosoma brucei gambiense Trypanosoma brucei rhodesiense Laboratory diagnosis (all species) Routine methods Antigen detection Antibody detection Molecular methods Therapy American trypanosomiasis Trypanosoma cruzi General characteristics Pathogenesis and spectrum of disease Laboratory diagnosis Routine methods. Molecular methods. Xenodiagnosis. Antigen detection. Serologic tests. Histology. Therapy Leishmania spp. General characteristics Pathogenesis and spectrum of disease Laboratory diagnosis Serologic tests Molecular methods Therapy Bibliography 49 Protozoa from other body sites Objectives Free-living amoebae Naegleria fowleri General characteristics Pathogenesis and spectrum of disease Laboratory diagnosis Routine methods Other methods Therapy Acanthamoeba spp. General characteristics Pathogenesis and spectrum of disease Granulomatous amoebic encephalitis Keratitis Laboratory diagnosis Routine methods Other methods Therapy Disseminated infections Acanthamoeba keratitis Balamuthia mandrillaris General characteristics Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Molecular methods (free-living amoebae) Results reporting (free-living amoebae) Trichomonas vaginalis General characteristics Pathogenesis and spectrum of disease Laboratory diagnosis Wet mounts Stained smears Culture Antigen detection Molecular methods Therapy Pentatrichomonas hominis General characteristics Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Toxoplasma gondii General characteristics Pathogenesis and spectrum of disease Immunocompetent individuals Immunocompromised individuals Congenital infections Ocular infections Laboratory diagnosis Molecular methods Therapy Bibliography 50 Intestinal nematodes Objectives Ascaris lumbricoides General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Enterobius vermicularis General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Strongyloides stercoralis General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Serologic testing Molecular methods Therapy Prevention Trichostrongylus spp. General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Trichuris trichiura General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Capillaria philippinensis General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Hookworms Epidemiology Ancylostoma duodenale General characteristics Pathogenesis and spectrum of disease Necator americanus General characteristics Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Results and reporting Bibliography 51 Tissue nematodes Objectives Trichinella spiralis General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Serologic testing Molecular methods Therapy Prevention Toxocara canis (visceral larva migrans) and toxocara cati (ocular larva migrans) General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Serologic testing Therapy Prevention Ancylostoma braziliense or ancylostoma caninum (cutaneous larva migrans) General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Dracunculus medinensis General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Parastrongylus cantonensis (cerebral angiostrongyliasis) General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Parastrongylus costaricensis (abdominal angiostrongyliasis) General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Gnathostoma spinigerum General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Dirofilaria immitis and other species General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Bibliography 52 Blood nematodes Objectives Wuchereria bancrofti General characteristics Epidemiology Pathogenesis and spectrum of disease Endosymbiont Laboratory diagnosis Direct detection Serologic testing Molecular methods Brugia malayi and brugia timori General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Loa loa General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Direct detection Serologic testing Molecular methods Therapy Prevention Onchocerca volvulus General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Direct detection Serologic testing Molecular methods Therapy Prevention Mansonella spp. (m. ozzardi, m. streptocerca, m. perstans) General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Bibliography 53 Intestinal cestodes Objectives Diphyllobothrium latum General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Dipylidium caninum General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Hymenolepis nana General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Hymenolepis diminuta General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Taenia solium General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Taenia saginata General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Bibliography 54 Tissue cestodes Objectives Taenia solium General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Echinococcus granulosus General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Echinococcus multilocularis General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Taenia multiceps and other species General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Spirometra mansonoides General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Therapy Prevention Bibliography 55 Intestinal trematodes Objectives Fasciolopsis buski General characteristics Epidemiology Pathogenesis and spectrum of disease Therapy and prevention Heterophyes and metagonimus yokogawai General characteristics Epidemiology Pathogenicity and spectrum of disease Prevention Laboratory diagnosis Treatment Bibliography 56 Liver and lung trematodes Objectives The liver flukes General characteristics Epidemiology and life cycle Pathogenesis and spectrum of disease Laboratory diagnosis Serologic testing Therapy and prevention The lung flukes General characteristics Epidemiology and life cycle Pathogenesis and spectrum of disease Laboratory diagnosis Serologic testing Treatment and prevention Bibliography 57 Blood trematodes Objectives General characteristics Epidemiology Pathology and spectrum of disease Laboratory diagnosis Therapy Prevention Bibliography Part V Mycology 58 Overview of fungal identification methods and strategies Objectives Epidemiology General features of the fungi Taxonomy of the fungi Clinical classification of the fungi Practical working schema Pathogenesis and spectrum of disease Laboratory diagnosis Collection, transport, and culturing of clinical specimens Respiratory tract secretions Cerebrospinal fluid Blood Eye (corneal scrapings or vitreous humor) Hair, skin, and nail scrapings Vaginal Urine Tissue, bone marrow, and sterile body fluids Culture media and incubation requirements Direct microscopic examination Serologic testing Molecular methods Matrix-assisted laser desorption ionization mass spectrometry General considerations for the identification of yeasts General considerations for the identification of molds General morphologic features of the molds Clinical relevance for fungal identification Laboratory safety Prevention Bibliography 59 Hyaline molds, mucorales, entomophthorales, dermatophytes, and opportunistic and systemic mycoses Objectives The mucorales General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Specimen collection, transport, and processing Direct detection methods Stains Antigen-protein Molecular methods Cultivation Approach to identification Serologic testing Matrix-assisted laser desorption ionization time-of-flight mass spectrometry The entomophthorales General characteristics Epidemiology and pathogenesis Spectrum of disease Laboratory diagnosis Specimen collection, transport, and processing Direct detection methods Antigen-protein Molecular methods Cultivation Approach to identification Serologic testing The dermatophytes General characteristics Epidemiology and pathogenesis Spectrum of disease Trichophyton spp. Laboratory diagnosis Specimen collection, transport, and processing Direct detection methods Stains Antigen-protein Molecular methods Cultivation Approach to identification Trichophyton spp. Microsporum spp. Epidermophyton sp. Serologic testing The opportunistic mycoses General characteristics Epidemiology and pathogenesis Aspergillus spp. Pathogenesis and spectrum of disease Aspergillus spp. Fusarium spp. and other hyaline septate opportunistic molds Laboratory diagnosis Specimen collection, transport, and processing Direct detection methods Stains Antigen-protein Molecular methods Matrix-assisted laser desorption ionization time-of-flight mass spectrometry Cultivation Approach to identification Aspergillus spp. Serologic testing Fusarium spp. Geotrichum candidum Acremonium spp. Penicillium spp. and talaromyces marneffei Paecilomyces spp. Purpureocillium spp. Scopulariopsis spp. Serologic testing Systemic mycoses General characteristics Epidemiology Blastomyces spp. Coccidioides spp. Emmonsia spp. Histoplasma capsulatum Paracoccidioides brasiliensis Talaromyces marneffei Sporothrix spp. Pathogenesis and spectrum of disease Blastomyces spp. Coccidioides spp. Emmonsia spp. Histoplasma capsulatum Paracoccidioides brasiliensis Talaromyces marneffei Sporothrix spp. Laboratory diagnosis Specimen collection, transport, and processing Direct detection methods Stains Blastomyces spp. Coccidioides spp. Emmonsia spp. Histoplasma capsulatum. Paracoccidioides brasiliensis. Talaromyces marneffei.  Sporothrix spp. Antigen-protein Molecular methods Cultivation Blastomyces dermatitidis. Coccidioides spp. Emmonsia spp. Histoplasma capsulatum. Paracoccidioides brasiliensis.  Talaromyces marneffei.  Sporothrix spp. Approach to identification Blastomyces dermatitidis Coccidioides spp. Emmonsia spp. Histoplasma capsulatum Paracoccidioides brasiliensis Talaromyces marneffei Sporothrix spp. Serologic testing References Bibliography 60 Dematiaceious (melanized) molds Objectives General characteristics Epidemiology and pathogenesis Superficial infections Mycetoma Chromoblastomycosis Phaeohyphomycosis Pathogenesis and spectrum of disease Laboratory diagnosis Specimen collection, transport, and processing Direct detection method Stains Superficial infections Chromoblastomycosis Mycetoma and phaeohyphomycosis Serologic testing Molecular methods Matrix-assisted laser desorption ionization time-of-flight mass spectrometry Cultivation Superficial infections Mycetoma White grain mycetoma. Black grain mycetoma. Chromoblastomycosis Phaeohyphomycosis Approach to identification Superficial infections Mycetoma White grain mycetoma: pseudallescheria boydii and acremonium spp. Black grain mycetoma: exophiala jeanselmei, curvularia spp., and madurella spp. Chromoblastomycosis: cladosporium, phialophora, and fonsecaea spp. Phaeohyphomycosis: alternaria, bipolaris, cladophialophora, curvularia, exophiala, exserohilum, and phialophora spp. Alternaria spp. Bipolaris spp. Cladophialophora spp. Curvularia spp. Exophiala spp. Exserohilum spp. Antifungal susceptibilities Bibliography 61 Opportunistic atypical fungus: Objectives General characteristics Epidemiology Pathogenesis and spectrum of disease Laboratory diagnosis Specimen collection and transport Specimen processing Direct detection methods Stains Direct detection of (1-3)-beta-d-glucan Molecular methods Cultivation Approach to identification Serologic testing References Bibliography 62 The yeasts Objectives General characteristics Epidemiology Blastoschizomyces spp. Candida spp. Cryptococcus spp. Malassezia, pseudozyma, rhodotorula, saccharomyces, sporobolomyces, and trichosporon spp. Pathogenesis and spectrum of disease Blastoschizomyces spp. Candida albicans Non-albicans candida Cryptococcus neoformans Genus cryptococcus Cryptococcus gattii Malassezia spp. Pseudozyma spp. Rhodotorula spp. Saccharomyces cerevisiae Sporobolomyces spp. Trichosporon spp. Laboratory diagnosis Specimen collection, transport, and processing Stains Candida spp. Cryptococcus spp. Malassezia spp. Trichosporon spp. Antigen detection Molecular methods Cultivation Candida spp. Cryptococcus spp. Trichosporon spp. Malassezia spp. Approach to identification Candida spp. Germ tube test Cryptococcus neoformans Serologic testing Rapid urease test Rapid trehalose test Trichosporon spp. Malassezia spp. Commercially available yeast identification systems Multiple species identification systems Api-20c aux Microscan rapid ys Vitek biochemical cards Other multiple species systems Chromagar candida Matrix-assisted laser desorption ionization time-of-flight Conventional yeast identification methods Cornmeal agar morphology Carbohydrate utilization Phenoloxidase detection using niger seed agar Reference Bibliography 63 Antifungal susceptibility testing, therapy, and prevention Objectives Antifungal susceptibility testing Antifungal therapy and prevention Polyene macrolide antifungals Amphotericin b Nystatin Griseofulvin 5-fluorocytosine (flucytosine) Azole antifungal drugs Clotrimazole and miconazole Fluconazole Ketoconazole Itraconazole Voriconazole Posaconazole Echinocandins Allylamines Terbinafine (lamisil) and naftifine Selenium sulfide Potassium iodide Bibliography Part VI Virology 64 Overview of the methods and strategies in virology Objectives General characteristics Viral structure Virus taxonomy Viral replication Epidemiology Pathogenesis and spectrum of disease Prevention and therapy Antiviral agents Viruses that cause human diseases Laboratory diagnosis Designing a clinical virology laboratory Specimen selection and collection General principles Throat, nasopharyngeal swab, or aspirate Bronchial and bronchoalveolar washes Rectal swabs and stool specimens Urine Skin and mucous membrane lesions Sterile body fluids other than blood Blood Bone marrow Tissue Genital specimens Serum for antibody testing Specimen transport and storage Specimen processing General principles Processing based on specimen type Lip and genital specimens Urine Stool Respiratory tract Specimens from neonatal patients Cerebrospinal fluid Blood Processing based on requests for specific viruses Arboviruses Cytomegalovirus Enteroviruses Epstein-barr virus Hepatitis viruses Herpes simplex virus Human immunodeficiency virus and other retroviruses Influenza a and b viruses Pediatric respiratory viruses Gastroenteritis viruses Torch Varicella-zoster virus Virus detection methods Cytology and histology Electron microscopy Immunodiagnosis (antigen detection) Enzyme-linked virus-inducible system Molecular methods Cell culture Conventional cell culture Shell vial cell culture Identification of viruses detected in cell culture Serologic testing General principles Immune status testing Serology panels Preservation and storage of viruses Bibliography 65 Viruses in human disease Objectives Viruses in human disease Adenoviruses Arenaviruses Bunyaviruses Caliciviruses Coronaviruses Filoviruses Flaviviruses Hepevirus Hepadnaviruses Herpes viruses Orthomyxoviruses Papillomaviruses Paramyxoviruses Parvoviruses Picornaviruses Polyomaviruses Poxviruses Reoviruses Retroviruses Rhabdoviruses Togaviruses Miscellaneous viruses Interpretation of laboratory test results Viruses in tissue and body fluids Viruses in the respiratory tract Viruses in the eye Detection of epstein-barr virus Detection of enteroviruses Detection of hepatitis viruses Detection of varicella-zoster virus and herpes simplex virus Detection of cytomegalovirus Detection of human immunodeficiency virus Prions in human disease Bibliography 66 Antiviral therapy, susceptibility testing, and prevention Objectives Antiviral therapy Antiviral resistance Methods of antiviral susceptibility testing Phenotypic assays Plaque reduction assay Dye uptake assay Deoxyribonucleic acid hybridization Enzyme immunoassay Flow cytometry Neuraminidase inhibition assay Recombinant virus assays Genotypic susceptibility assays Pyrosequencing Next generation sequencing Human immunodeficiency virus Influenza Prevention of other viral infections Vaccination Immune prophylaxis and therapy Eradication Bibliography Part VII Diagnosis by Organ System 67 Bloodstream infections Objectives General considerations Etiology Bacteria Fungi Parasites Viruses Types of bacteremia Types of bloodstream infections Intravascular infections Endocarditis Mycotic aneurysm and suppurative thrombophlebitis Intravenous catheter–associated bacteremia. Extravascular infections Clinical manifestations Immunocompromised patients Detection of bacteremia Specimen collection Preparation of the site Antisepsis Precautions Specimen volume Adults Children Number of blood cultures Timing of collection Miscellaneous matters Anticoagulation Dilution Blood culture media Types of blood culture bottles Culture techniques Conventional blood cultures Incubation conditions Self-contained subculture system Lysis centrifugation Instrument-based systems Bactec systems Bact/alert microbial detection system Versa trek system Techniques to detect intravenous catheter–associated infections Handling positive blood cultures Interpretation of blood culture results Special considerations for other relevant organisms isolated from blood Hacek (aacek) bacteria Campylobacter and helicobacter Fungi Mycobacteria Brucella Spirochetes Borrelia Leptospira Vitamin b6–dependent streptococci Mycoplasma hominis Bartonella Bibliography 68 Infections of the lower respiratory tract Objectives General considerations Anatomy Pathogenesis of the respiratory tract: Basic concepts Host factors Microorganism virulence factors Adherence Toxins Microorganism growth Avoiding the host response Diseases of the lower respiratory tract Bronchitis Acute Chronic versus acute Bronchiolitis Pneumonia Pathogenesis Clinical manifestations Epidemiology and etiologic agents Community-acquired pneumonia Children. Young adults. Adults (viral pneumonia) Adults (fungal pneumonia) Chronic lower respiratory tract infections Immunocompromised patients Patients with neoplasms. Transplant recipients. Patients with human immunodeficiency virus. Pleural infections Laboratory diagnosis of lower respiratory tract infections Specimen collection and transport Sputum Expectorated Induced Endotracheal or tracheostomy suction specimens Bronchoscopy Transtracheal aspirates Other invasive procedures Specimen processing Direct visual examination Routine culture Bibliography 69 Upper respiratory tract infections and other infections of the oral cavity and neck Objectives General considerations Anatomy Pathogenesis Diseases of the upper respiratory tract, oral cavity, and neck Upper respiratory tract Laryngitis Laryngotracheobronchitis Epiglottitis Pharyngitis, tonsillitis, and peritonsillar abscesses Pharyngitis and tonsillitis Clinical manifestations. Pathogenesis. Epidemiology and etiologic agents. Peritonsillar abscesses Rhinitis Miscellaneous infections caused by other agents Corynebacterium diphtheriae Bordetella pertussis Klebsiella spp. Oral cavity Stomatitis Thrush Periodontal infections Types Etiologic agents Salivary gland infections Neck Diagnosis of upper respiratory tract infections Collection and transport of specimens Direct visual examination or detection Culture Streptococcus pyogenes (beta-hemolytic group a streptococci) Corynebacterium diphtheriae Bordetella pertussis Neisseria spp. Epiglottitis Diagnosis of infections in the oral cavity and neck Collection and transport Direct visual examination Culture Bibliography 70 Meningitis and other infections of the central nervous system Objectives General considerations Anatomy Coverings and spaces of the central nervous system Cerebrospinal fluid Routes of infection Diseases of the central nervous system Meningitis Purulent meningitis Pathogenesis. Clinical manifestations. Acute. Chronic. Epidemiology and etiologic agents of acute meningitis. Aseptic meningitis Encephalitis/meningoencephalitis Viral encephalitis Parasitic infections Brain abscess Shunt infections Laboratory diagnosis of central nervous system infections Meningitis Specimen collection and transport Initial processing Cerebrospinal fluid laboratory results Visual detection of etiologic agents Stained smear of sediment Wet preparation India ink stain Direct detection of etiologic agents Antigen Bacteria. Cryptococcus neoformans. Molecular methods Miscellaneous tests Culture Bacteria and fungi Parasites and viruses Brain abscess/biopsies Specimen collection, transport, and processing. Bibliography 71 Infections of the eyes, ears, and sinuses Objectives Eyes Anatomy Resident microbiota Diseases Pathogenesis Epidemiology and etiology of disease Blepharitis Conjunctivitis Keratitis Endophthalmitis Periocular Uveitis Other infections Laboratory diagnosis Specimen collection and transport Direct visual examination Culture Nonculture methods Ears Anatomy Resident microbiota Diseases, epidemiology, and etiology of disease Otitis externa (external ear infections) Otitis media (middle ear infections) Pathogenesis Laboratory diagnosis Specimen collection and transport Direct visual examination Culture and nonculture methods Sinuses Anatomy Diseases Pathogenesis Epidemiology and etiology of disease Laboratory diagnosis Matrix-assisted laser desorption ionization time-of-flight mass spectrometry Bibliography 72 Infections of the urinary tract Objectives General considerations Anatomy Resident microbiota of the urinary tract Infections of the urinary tract Epidemiology Etiologic agents Community-acquired Hospital- and health care–associated Miscellaneous Pathogenesis Routes of infection The host-pathogen relationship Types of infection and their clinical manifestations Urethritis Ureteritis Asymptomatic bacteriuria Cystitis Acute urethral syndrome Pyelonephritis Urosepsis Laboratory diagnosis of urinary tract infections Specimen collection Clean-catch midstream urine Straight catheterized urine Suprapubic bladder aspiration Indwelling catheter Specimen transport Screening procedures Gram or methylene blue stain Pyuria Indirect indices Nitrate reductase (greiss) test Leukocyte esterase test Catalase Automated and semiautomated systems General comments regarding screening procedures Urine culture Inoculation and incubation of urine cultures Interpretation of urine cultures Bibliography 73 Genital tract infections Objectives General considerations Anatomy Resident microbiota Sexually transmitted diseases and other genital tract infections Genital tract infections Sexually transmitted diseases and other lower genital tract infections Epidemiology and etiologic agents Routes of transmission Sexually transmitted Other routes Clinical manifestations Asymptomatic Dysuria Urethral discharge Lesions of the skin and mucous membranes Vaginitis Cervicitis Anorectal lesions Bartholinitis Infections of the reproductive organs and other upper genital tract infections Females Pelvic inflammatory disease Infections after gynecologic surgery Infections associated with pregnancy Males Gonorrhea Syphilis Laboratory diagnosis of genital tract infections Lower genital tract infections Urethritis, cervicitis, and vaginitis Specimen collection Urethral. Cervical and vaginal. Transport. Direct microscopic examination Culture Nonculture methods Genital skin and mucous membrane lesions Buboes Infections of the reproductive organs Pelvic inflammatory disease Miscellaneous infections Infections of neonates and human products of conception Bibliography 74 Gastrointestinal tract infections Objectives Anatomy Resident gastrointestinal microbiome Gastroenteritis Pathogenesis Host factors Microbial factors Primary pathogenic mechanisms Toxins Enterotoxins. Cytotoxins. Neurotoxins. Attachment. Invasion. Miscellaneous virulence factors Clinical manifestations Epidemiology Institutional settings Traveler’s diarrhea Foodborne and waterborne outbreaks Immunocompromised hosts Etiologic agents Other infections of the gastrointestinal tract Esophagitis Gastritis Proctitis Miscellaneous Laboratory diagnosis of gastrointestinal tract infections Specimen collection and transport General comments Stool specimens for bacterial culture Stool specimens for ova and parasites Stool specimens for viruses Miscellaneous specimen types Direct detection of agents of gastroenteritis in feces Wet mounts Stains Antigen detection Molecular methods Culture of fecal material for isolation of etiologic agents Bacteria Organisms for routine culture Routine culture methods Salmonella and shigella. Campylobacter. Enrichment broths. Laboratory diagnosis of clostridium difficile–associated diarrhea Bibliography 75 Skin, soft tissue, and wound infections Objectives General considerations Anatomy of the skin Function of the skin Prevalence, etiology, and pathogenesis Skin and soft tissue infections Infections of the epidermis and dermis Infections in or around hair follicles Infections in the keratinized layer of the epidermis Infections in the deeper layers of the epidermis and dermis Infections of the subcutaneous tissues Infections of the muscle fascia and muscles Necrotizing fasciitis Progressive bacterial synergistic gangrene Myositis Wound infections Postoperative infections Bites Burns Special circumstances regarding skin and soft tissue infections Infections related to vascular and neurologic problems Sinus tracts and fistulas Systemic infections and skin manifestations Laboratory diagnostic procedures Infections of the epidermis and dermis Erysipeloid Superficial mycoses and erythrasma Erysipelas and cellulitis Vesicles and bullae Infections of the subcutaneous tissues Infections of the muscle fascia and muscles Wound infections Postoperative Bites Burns Bibliography 76 Normally sterile body fluids, bone and bone marrow, and solid tissues Objectives Specimens from sterile body sites Fluids Pleural fluid Peritoneal fluid Primary peritonitis Secondary peritonitis Peritoneal dialysis fluid Pericardial fluid Joint fluid Bone Bone marrow aspiration or biopsy Bone biopsy Solid tissues Laboratory diagnostic procedures Specimen collection and transport Fluids and aspirates Bone Tissue Specimen processing, direct examination, and culture Fluids and aspirates Bone Solid tissue Bibliography Part VIII Clinical Laboratory Management 77 Quality in the clinical microbiology laboratory Objectives Quality program Specimen collection and transport Standard operating procedure manual Personnel Reference laboratories Patient reports Proficiency testing Performance checks Instruments Commercially prepared media exempt from quality control User-prepared and nonexempt, commercially prepared media Antimicrobial susceptibility tests Stains and reagents Antisera Kits Maintenance of quality control records Maintenance of reference quality control stocks Bacteriology Mycology Mycobacteriology Virology Parasitology Quality assurance program Types of quality assurance audits Conducting a quality assurance audit Continuous daily monitoring Bibliography 78 Infection control Objectives Incidence of health care–associated infections Types of health care–associated infections Urinary tract infections Lung infections Surgical site infections Central line–associated bloodstream infection Emergence of antibiotic-resistant microorganisms Hospital infection control programs Role of the microbiology laboratory Characterizing strains involved in an outbreak Preventing health care–associated infections Surveillance methods Bibliography 79 Sentinel laboratory response to bioterrorism Objectives General considerations Bio crime Government laws and regulations Biosecurity Laboratory response network Role of the sentinel laboratory Bibliography Glossary Index A B C D E F G H I J K L M N O P Q R S T U V W X Y Z