Wallach's Interpretation of Diagnostic Tests: Pathways to Arriving at a Clinical Diagnosis (459 page)

Proteome
: All the proteins expressed by the genome in a given cell or tissue at a given time under specific conditions.

Proteomics
: Field of biochemistry/genetics encompassing the comprehensive analysis and cataloging of the structure and function of the proteome.

Pyrosequencing
: Method for sequencing single-stranded DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step by detecting the activity of DNA polymerase (a DNA-synthesizing enzyme) with another chemiluminescent enzyme.

Real-time PCR (quantitative PCR)
: Used to quantify DNA or messenger RNA (mRNA) in a sample by using sequence specific, fluorescently labeled primers to determine the relative (between tissue or relative to a specific housekeeping gene) or absolute number of copies of a particular DNA or RNA sequence in a sample. The quantification arises by measuring the amount of amplified product at each stage during the PCR cycle.

Restriction enzymes (RE)
: Part of the system that bacteria use to protect themselves against viruses by cutting up DNA at specific sequences. Many RE are used to digest DNA into specific fragments that can be used for genotyping.

Reverse hybridization (line probe assay; LIPA)
: Biotinylated amplified PCR product is hybridized to oligonucleotides that are immobilized as parallel lines on membrane (e.g., nitrocellulose) strips. Unhybridized PCR product is washed off the strip, and a reporter such as alkaline phosphatase–labeled streptavidin conjugate is bound to the biotinylated hybrid, followed by chromogen substrate (such as BCIP/ NBT) visualization of the banding pattern. The top band of the membrane strip usually contains a positive control.

Reverse transcription
: Synthesis of a complementary DNA sequence from an RNA template; uses an enzyme, reverse transcriptase, which is an RNA-dependent DNA polymerase.

Restriction fragment length polymorphism (RFLP) analysis
: Procedure in which the DNA sample is digested into smaller fragments by restriction enzymes, and the resulting fragments are separated according to their lengths. RFLP is used for determination of mutations and paternity testing.

Sequence analysis
: Determination of the nucleotide sequence in a DNA sample. Sequencing is a gold standard for mutation analysis detection of single base changes and microdeletions and/or microinsertions.

Single nucleotide polymorphism (SNP)
: Change in which a single nucleotide in the genomic DNA differs from the usual nucleotide at that position. Some SNPs are responsible for disease, whereas other SNPs are variations without functional significance.

Southern blot
: Used to identify and identify electrophoresed size-separated, membrane-immobilized DNA sequences that are complementary to a DNA fragment used as a hybridization probe.

Single-stranded conformation polymorphism (SSCP)
: Detects changes in DNA sequence based on differences in electrophoretic mobility under nondenaturing conditions and constant temperature. The method can be used for mutation screening but requires mutation confirmation by another method such as sequencing.

Targeted mutation analysis
: Testing for either one or more specific mutations.

Temperature gradient gel electrophoresis (TGGE)
: Detects changes in DNA sequence based on differences in energy required for separation of double-stranded DNA fragments of the same size into single-stranded DNA strands (unzipping) during electrophoresis on a polyacrylamide gel using only a temperature gradient (DGGE also uses denaturants). A confirmatory test is required for mutation analysis.

Transcription-mediated amplification (TMA):
Isothermal target nucleic acid amplification method that uses RNA transcription (using RNA polymerase) and DNA synthesis (using reverse transcriptase) to produce an RNA amplicon from a target nucleic acid. TMA can be used to amplify both an RNA and DNA, and produces 100–1,000 copies per cycle; in contrast to PCR and LCR that produce only two copies per cycle.

Chapter
11

Infectious Diseases

Michael J. Mitchell

Infectious Diseases Caused by Bacterial Pathogens

Acinetobacter Infection

Anaplasmosis and Ehrlichiosis

Anthrax (
Bacillus anthracis
)

Bartonellosis

Bordetella pertussis

Botulism (
Clostridium botulinum
)

Brucella

Burkholderia
Infections

Campylobacter
Gastroenteritis

Chlamydia
and
Chlamydophila
Infections

Clostridial Infections: General

Clostridial Gas Gangrene, Cellulitis, and Puerperal Sepsis

Clostridium difficile
Infection (CDI) and Associated (Pseudomembranous) Colitis

Clostridium tetani
Infection

Diphtheria

Enterococcal Infections

Escherichia coli
Infection

Francisella tularensis
Infection

Haemophilus
Infections

Helicobacter pylori
Infection

Klebsiella pneumoniae
Infection

Listeria
Infection

Lyme Disease

Mycoplasma pneumoniae
and
Ureaplasma urealyticum
Infections

Neisseria gonorrhoeae
Infection

Neisseria meningitidis
Infection

Pasteurella multocida
Infection

Pseudomonas aeruginosa
Infection

Q Fever (
Coxiella burnetii
)

Rocky Mountain Spotted Fever

Salmonella
and
Shigella
Infections

Staphylococcus aureus
Infection

Stenotrophomonas maltophilia
Infection

Streptococcus agalactiae
(Group B) Infection

Streptococcus pneumoniae
Infection

Streptococcus pyogenes
(Group A) Infection

Treponemal Disease: Syphilis

Vibrio
Infection

Yersinia
Infection

Infectious Diseases Caused by Acid-Fast Bacterial Pathogens (AFB)

Mycobacterium tuberculosis

Nocardia
Infection

Rapidly Growing Mycobacteria

Slow-Growing, Nontuberculous Mycobacteria

Diseases Caused by Fungal Pathogens

Aspergillosis

Blastomycosis

Candidiasis

Coccidioidomycosis

Cryptococcosis (
Cryptococcus neoformans
)

Fusariosis

Histoplasmosis

Mucormycosis

Paracoccidioidomycosis (
Paracoccidioides brasiliensis)

Pneumocystis jirovecii
(Formerly
P. carinii
)

Sporotrichosis

Infectious Diseases Caused by Viral Pathogens

Cytomegalovirus Infection

Encephalitis Viruses

Enterovirus, Coxsackievirus, and Echovirus

Epstein-Barr Virus Infections

Hepatitis Viruses

Herpes Simplex Virus Infections

HIV-1 Infection and Acquired Immunodeficiency Syndrome

Human Papillomavirus (HPV) Infection

Mumps

Norovirus Gastroenteritis (Norwalk Agent)

Parvovirus B19 (Erythema Infectiosum, Fifth Disease, Transient Aplastic Anemia)

Poliomyelitis

Respiratory Viruses

Rubella (German Measles)

Rubeola (Measles)

Smallpox (Variola Virus)

Varicella-Zoster Virus Infections

Infectious Diseases Caused by Parasitic Pathogens

Amebiasis

Ascariasis (
Ascaris lumbricoides
)

Babesiosis

Beef Tapeworm (
Taenia saginata
)

Cryptosporidiosis and Other Coccidia Infections

Cysticercosis (Pork Tapeworm,
Taenia solium
)

Giardiasis

Larva Migrans (Cutaneous and Visceral)

Leishmaniasis

Malaria

Microsporidiosis

Pinworm Infection (
Enterobius vermicularis
)

Schistosomiasis

Strongyloidiasis (
Strongyloides stercoralis
)

Toxoplasmosis

Trichinosis (Trichinellosis;
Trichinella spiralis
)

Trichomoniasis

T
his Chapter reviews some of the major infectious diseases caused by bacterial, fungal, viral, and parasitic pathogens. Pathogenic agents are arranged in alphabetical order in each section. Information regarding infections of specific organ systems may be found in the appropriate organ-specific Chapters. For example, information regarding TB can be found in Chapter
13
, Respiratory, Metabolic, and Acid–Base Disorders.

The diagnosis of specific infectious diseases is typically based on a combination of clinical signs and symptoms, exposure history, specific risk factors, and laboratory testing. Molecular diagnostic testing is playing an increasingly important role in the diagnosis of infectious diseases. See Chapter
17
, Infectious Disease Assays, for detailed information regarding specific diagnostic testing for infectious diseases. Refer to
http://www.fda.gov/MedicalDevices/ProductsandMedicalProcedures/InVitroDiagnostics/ucm330711.htm
for an updated listing of FDA-approved nucleic acid based diagnostic tests.

   
INFECTIOUS DISEASES CAUSED BY BACTERIAL PATHOGENS