Chapter 1 Introduction to Clinical Microbiology © Alex011973/Shutterstock, Inc. Chapter OutlIne Classification and Taxonomy The Role of Clinical Microbiology Characteristics of Eukaryotes and Prokaryotes The Infectious Process Key terMs Acquired immunity Infection Antibody Infectious disease Antigen Inflammatory response Asymptomatic carrier Innate immunity Cell-mediated immunity (CMI) Normal flora Colonization Nosocomial Endotoxin Pathogen Exotoxin Phagocytosis Humoral immunity Pili Immunoglobulin Superinfection Immunosuppressive learnIng ObjeCtIves 1. Discuss the purpose of clinical microbiology. 7. Define the following terms: 2. Describe the binomial system of taxonomy a. Infection and discuss how phenotypic and molecular b. Infectious disease characteristics are used to classify bacteria. c. True pathogen 3. Identify and give the function of the bacterial cell d. Opportunistic pathogen components. e. Nosocomial infection 4. Differentiate the gram-positive cell wall from the f. Endogenous infection gram-negative cell wall. g. Exogenous infection 5. State the function of pili, fimbriae, flagella, and the h. Asymptomatic carriage (carriers) capsule. i. Colonization 6. Describe the important metabolic activities of the 8. Define and contrast: bacterial cell. a. endemic and epidemic b. disease prevalence and incidence 9781284032314_CH01_001_016.indd 1 13/02/14 11:53 AM 2 CHAPTER 1 Introduction to Clinical Microbiology 9. Define normal flora and discuss its role in each of the d. Humoral immunity following sites: e. Cell-mediated immunity a. Mouth and oral cavity 12. Describe the function of B and T cells in the immune b. Nasopharynx response: c. Stomach and small intestine a. List and summarize the characteristics of the d. Colon human immunoglobulin classes. 10. List and describe the major routes of infection. b. List and state the function of four populations of 11. Describe the following host defense mechanisms: T cells. a. Innate (natural) immunity 13. Define and describe endotoxins and exotoxins. b. Inflammatory response 14. List the signs of microbial infection. c. Acquired immunity 15. List the laboratory procedures that might be requested to identify infectious disease. The purpose of clinical microbiology is to isolate and iden- Classification and taxonomy tify pathogenic microorganisms. Clinical microbiologists work with clinicians and other personnel to assist in the The classification of organisms into categories based on diagnosis, management, and treatment of infectious dis- genotypic and phenotypic characteristics is known as tax- ease. The microbiology laboratory can provide the phy- onomy. Historically, classification has been based mostly sician with information from direct smears and stains, on observable properties such as morphology, biochemical cultures, molecular analysis, serological testing, and an- characteristics, and antigenic relationships. Examples of tibiotic susceptibility testing. The physician also relies on phenotypical characteristics used to classify microorgan- the patient’s medical history; physical examination; and isms are shown in BOX 1-1. results of X-rays, laboratory tests, and epidemiological in- This phenotypical classification is being replaced with formation (such as previous infections, travel, and illness systems based on genetic homology. Although these sys- in the family) to aid in the diagnosis of infectious disease. tems are more precise, at times, they do not conform to This chapter provides an introduction to clinical mi- classification based on phenotypic characteristics. Genetic crobiology, including a review on taxonomy, bacterial homology includes classification based on DNA base com- structure, and metabolism. Also discussed are the con- position and ratio. The cytosine and guanine content (CG) cepts of pathogens and normal flora and the infectious to total base content is used as an indicator of relatedness. process, including symptoms and routes of infection. A Nucleic acid sequence analysis uses the order of bases along summary of the inflammatory process and immunity is the DNA or RNA sequence and determines similar se- discussed and important definitions provided. quences between two organisms. BOX 1-1 phenotypical Classification Characteristics Macroscopic morphology: Size, texture, color, elevation Microscopic morphology: Size, shape (cocci, bacilli), arrangement (pairs, chains, clusters) Staining characteristics: Gram-stain reaction (positive/negative), acid fastness Environmental requirements: Temperature optimum, oxygen needs, pH needs, carbon dioxide needs, need/able to withstand NaCl Nutritional requirements: Use carbon or nitrogen substrates Resistance profiles: Inherent resistance to antibiotics, chemicals Antigenic properties: Serological or immunological methods (Lancefield groups of Streptococcus, properties of capsules) 9781284032314_CH01_001_016.indd 2 13/02/14 11:53 AM Characteristics of Eukaryotes and Prokaryotes 3 When identifying microorganisms, the key features are outlined based on genotypic characteristics, including BOX 1-2 example of Classification genes and nucleic acids and phenotypic characteristics, Family: Microcococceae which are observable. The hierarchy for classification is summarized below, beginning with the largest division, or Genus: Staphylococcus kingdom, and ending with the smallest division, or species. Species: aureus Kingdom Accepted abbreviation: S. aureus Division Informal: staphylococci Class Order Family information on the organism is investigated, and the or- Genus ganism may or may not be reclassified or renamed. When Species a new name is accepted, the written format is “new name The species is the most basic taxonomic group and encom- (old name)” until sufficient time has elapsed to recognize passes bacterial strains with common genetic, physiologic, the change. For example, Enterococcus faecalis was for- and phenotypic characteristics. There may be subgroups merly classified in the genus Streptococcus; when it was re- within the species, which are known as subspecies. Below classified, Enterococcus (Streptococcus) faecalis was written the subspecies level, there may be microorganisms that for clarification. BOX 1-2 gives an example of nomenclature. share specific minor characteristics; these are known as biotypes, subtypes, or strains or genotypes. Strains or sub- types are genetic variants of the microorganism. Differ- Characteristics of eukaryotes ent species with many important features in common are and prokaryotes known as a genus (genera). Genera are based on genetic and phenotypic characteristics among several species. It Eukaryotic cells contain membrane-enclosed structures, is usually not practical in microbiology to classify similar which have specific functions. Fungi and parasites are cat- genera into higher taxonomic levels. However, at times, egorized as eukaryotes. Eukaryotic cells have a cytoskel- grouping into families may be helpful. eton that supports the cell and also various organelles, In the binomial system of nomenclature, two names, such as the nucleus, mitochondria, endoplasmic reticu- the genus and species, are used. These are generally derived lum, Golgi bodies, and lysosomes. Bacterial cells are pro- from the Latin or Greek language. Both the genus and species karyotic, which means that they do not contain organelles names should be italicized or underlined; the genus name is enclosed in membranes. Prokaryotes are unicellular or- always capitalized and the species name is never capitalized. ganisms without a nuclear membrane, mitochondria, en- Accepted abbreviations include the uppercase form of the doplasmic reticulum, or Golgi bodies. Bacteria multiply first letter of the genus with a period. Informal names are asexually, and all cellular functions occur in either the written in lower case without italics or underlining. cytoplasm or cytoplasmic membrane of the bacterial cell. Proposed changes in nomenclature are examined by TABLE 1-1 summarizes the characteristics of eukaryotic the International Journal for Systematic Bacteriology. New and prokaryotic organisms. TABLE 1-1 Comparing the Characteristics of Eukaryotic and Prokaryotic Cells Eukaryotes Prokaryotes Microorganisms included Algae, fungi, protozoa Bacteria Nucleus Enclosed in nuclear membrane No nuclear membrane Mitochondria Present Absent Golgi bodies Present Absent Endoplasmic reticulum Present Absent Ribosomes 80S (60S + 40S) 70S (50S + 30S) 9781284032314_CH01_001_016.indd 3 13/02/14 11:53 AM 4 CHAPTER 1 Introduction to Clinical Microbiology Bacterial cells range from 1 μm to 3 μm in length and ribosomes, the DNA chromosome, mRNA, proteins and thus are not visible to the human eye without the aid of a metabolites, nucleoid, and plasmids. The cytosol contains microscope. Bacteria that are round are known as cocci; many enzymes and is the site of most metabolic processes cocci may arrange in pairs, chains, or clusters. Bacteria for the bacterial cell. The bacterial chromosome is one that have a rod shape are known as bacilli, and those with double-stranded circle contained in a discrete area of the a spiral form are known as spirochetes. cytoplasm, known as the nucleoid. The DNA is not con- Typical morphologies of bacteria are shown in tained within a nucleus, and there are no histones. Plas- FIGURE 1-1. mids, which are small, circular extrachromosomal DNA may also be found in the cytoplasm. Plasmids play a role baCterIal CompOnents in the development of antibiotic resistance. Bacterial cells contain a number of