1. Clinical Microbiology
Vocabulary

2. Glossary Aerobic- requiring oxygen
Anaerobic- growing only in the absence of oxygen
Antibiotic susceptibility testing- determining the susceptibility of microorganisms to specific antibiotics
Bacillus- rod-shaped bacteria
Coccus- spherical bacterium
Colony- defined mass of bacteria assumed to have grown from a single organism
Communicable- able to be transmitted directly or indirectly from one individual to an other
Culture- growth of microorganisms in a special medium; the process of growing microorganisms in the laboratory
DNA- nucleic acid found primarily in the nucleus of all living cells that carries genetic information; deoxyribonucleic acid
Fastidious organism- organism that requires special nutritional factors to survive
Fission- asexual reproduction of a microorganism
Formalin- solution of formaldehyde used as fixative or preservative
Gram-negative- designation for bacteria that lose the crystal violet (purple stain) and retain the safranin (red stain) in the gram stain procedure

3. Introduction
Microbiology is the study of living organisms of microscopic size. Louis Pasteur first used the term in the 1860s. Microorganisms were first observed in 1675 by Anthony van Leeuwenhoek, a Dutchman. The term “microbe” was introduced in 1878 to refer to these organisms. At present the term “microorganism” is common usage.
All living things are classified according to international rules of nomenclature.
Species of organisms are given two part names:
genus – which the organism belongs and it is written with the first letter capitalized.
specific epithet – uncapitalized name
Clinical microbiology encompasses the study of viruses, fungi, bacteria, and parasites. Test are included to isolate and identify these microorganisms. In a large hospital laboratory or reference laboratory, each of these specialties might be in a different department. However in a small laboratory may have a single microbiology department responsible for bacteriology, virology, parasitology, and mycology testing.

4. Vocabulary Aerobic – required oxygen.
Anaerobic – growing only in the absence of oxygen.
Antibiotic susceptibility testing – determining the susceptibility of microorganisms to specific antibiotics.
Bacillus – rod-shaped bacterium
Coccus – spherical bacterium
Colony - defined mass of bacteria assumed to assumed to have grown form a single organism
Communicable – able to be transmitted directly of indirectly from one individual to another.
Culture – growth of microorganisms in a special medium; the process of growing microorganisms in the laboratory.
DNA – nucleic acid found primarily in the nucleus of all living cells that carries genetic information; deoxyribonucleic acid.
Fastidious organism – organism that requires special nutritional factors to survive.
Fission – asexual reproduction of a microorganism.
Formalin – solution of formaldehyde used as a fixative of preservative.
Gram-negative – designation for bacteria that lose the crystal violet (purple stain) and retain the safranin (red stain) in the Gram stain procedure.
Gram-positive – designation for bacteria that retain the crystal violet( purple stain) in the Gram stain procedure.
Gram stain – differential stain used to classify bacteria.
Host – organism from which a parasite obtains nutrients and in which some or part of the parasites' life cycle is carried.
Hyphae – filaments of mold that makes up the mycelium.

5. Vocabulary Continued
Immunoassay – diagnostic method using antigen-antibody reactions.
Infection – pathological condition caused by growth of microorganisms.
Medium – substance used to provide nutrients for growing microorganisms.
Minimum inhibitory concentration (MIC) – minimum concentration of an antibiotic required to inhibit the growth of a microorganism.
Mycelium – mass of hyphae that , makes ups the vegetative body molds.
Mycosis – infection caused by fungi.
Normal flora – microorganisms normally present at a specific site.
Opportunistic pathogen – microorganisms that causes disease in eh host only when normal defense mechanisms are impaired or absent
Pathogen – organism or agent capable of causing disease in a host.
Progeny – offspring or descendants
RNA – nucleic acid found in all living cells that is that is important in protein synthesis; ribonucleic acid.
Spirochetes – motile bacteria with a helical or spiral shape.
Zone of inhibition – in the antibiotic susceptibility test, the area around an antibiotic disk that contains no bacterial growth.

6. Coccus (round) Bacillus (rod) Spirochete (spiral) 3 General groups
Certain kinds of cocci occur in pairs. They are called Diplococci.
Certain kinds of cocci are multicelled, branching patterns. They are called Filamentous.

7. Gram Stain is a procedure that stains bacteria differentially according to the composition of their cell walls.
Performed by applying crystal violet, gram’s iodine, a decolorizer, and a counterstain, safranin, to a bacterial smear.
Some bacteria retain the crystal violet. They are gram positive.
The ones that don’t retain the crystal violet are called Gram negative.

8. Clinical Bacteriology deals with the isolation and identification of bacterial pathogens, (those who are capable of producing disease).
Communicable diseases are diseases that spread from person to person.
Normal Flora are natural inhabitants of the human body.
Opportunistic pathogens invade the body and cause illness only when the body’s immune defenses are impaired or absent.

9. Specimen collection for bacteriology
Bacteria that require a specialized medium to grow and multiply are called Fastidious.
Bacteria that grow only in the presence of oxygen are Aerobic.
Bacteria that live and grow in the absence of oxygen are Anaerobic.

10. Usually procedures performed in a small laboratory or POL usually include:
Throat cultures
Rapid strep tests
Urine cultures
And occasionally Neisseria gonorrheae testing

11. Specimens Commonly Sent to Reference Laboratories
The reference laboratory should provide a procedure manual that explains how and when to use the various microbiology transport systems. Wound cultures, blood cultures, and sputum samples are usually sent to reference laboratories. Since a lot of organisms are hazardous, only well-trained personnel in specially equipped laboratories work with these specimens.

12. Identifying Bacteria
Test methods used by reference laboratories to aid in bacterial identification include microscopic morphology, colony appearance. Gram and other stain reactions, gene probes, and antibody reactions.

13. Antibiotic Susceptibility Testing
Once the microorganism causing the patient infection has been identified, antibiotic susceptibility must be determined. This may be accomplished by measuring the zone of inhibition around each antibiotic disk., which is the Bauer-Kirby method, or by finding the minimum inhibitory concentration (MIC) or various antibiotics. The Bauer-Kirby methods is performed on the surface of of a special medium called Mueller-Hinton no automated procedure is interpreted visually.

14. Susceptibility Testing Cont…
Bacteriology is an important part of the chemical laboratory.
Isolating and identifying the organism causing a patient’s illness is the first step in determining proper treatment. Although certain bacteria are usually found in particular infections, this is not always true: The technician should never eliminate testing for a particular organism just because it is not usually involved in that type of infection.

15. Parasitology
Clinical parasitology involves studying and identifying parasites, the disease they cause, and the disease treatments.
Parasites live in, on, or at the expense of another organism called an host organism.
It maybe is unicellular or multicellular
The may be present in the blood, bone marrow, and intestinal tract, liver, spleen, or any organ system.
Test usually performed in small laboratories include the cellophane tape test for pinworm and wet preps for a urogenital parasite, Trichomonas Vaginalis.

16. Detection of common intestinal parasites
Roundworms, flukes and hookworms, all of which are “helminths” are common intestinal parasites.
Larve ( immature forms) or adults of some helminths may be found. When protozoan parasites are suspected, the specimen is examined for cysts and trophozoites.
Stool examination for parasites- the O&P examination has traditionally consisted of three parts: a direct smear, a concentration, and a stained smear.
The Direct smear for the microscopic detection of protozoan motility requires a fresh stool specimen.
The concentration is for the protozoan cysts helminth eggs and larvae.
Stained smear is for identifying and confirming intestinal protozoa.
Immunoassays are also available to detect certain parasitic infections.

17. DeTEcti0N of triCH0m0NAS VaGiNAliS
The urogenital parasite, Trichomonas vaginalis, may be detected in urine, vaginal or urethral discharge, or prostatic secretions.
It may be visible by microscopic examination of secretions in a coverslip preparation or in a well-slide.
Trichomonas is recognized by its characteristic “twitching” motility.

18. deTEctiNG Bl00d and tiSSuE paRASitES
In the U.S. only a few organisms infect blood or other tissues. Worldwide, the most common blood parasite is malarial parasite, Plasmodium.
Blood parasites are discovered & identified by microscopically examining stained blood smears.
Specimens for blood & tissue parasites are usually sent to a reference laboratory.

19. diaGN0stiC TeSTinG in Vir0l0gY
Interest in diagnostic clinical virology has increased dramatically because of the demand for more rapid diagnosis of HIV and HPV.
In addition, increasing cases of hepatitis B and C, have helped motivate development of improved laboratory tests for viral infection.
The standard method for isolating and identifying viruses has been cell culture.
Patient serum can also tested for viral antibodies using the ELISA (enzyme-linked immunoabsorbent assay)

20. ViR0l0gY Virology is the study of viruses and the diseases they cause.
Common viruses that cause disease are influenza (flu), rubella, mumps, rubella (red measles), Epstein-Barr (infectious mononucleosis), and herpes.
Viruses are the most common cause of human infectious diseases. Some are known to cause cancer.
Viruses are not considered living cells and can only replicate by invading a cell.

21. Vir0l0gY c0nT’d
Once inside the cell, they cause the cell’s replication processes to make more virus offspring.
Each virus consists of a nucleic acid core and a protein coat called a capsid.
Living organisms contain both DNA and RNA, but a virus has only one or the other.
Viruses are much smaller than microorganisms and cannot be seen with a light microscope; electron microscopes are used to study them.

22. Diagnostic Kits for Virology
Diagnostic kits to test for several common viruses include latex slide agglutination tests for rubella and immunoassays to detect herpes simplex, influenza, rubella, and certain other viruses. Many of these kits are suitable for use in the smaller laboratory. A screening test called the Torch test is often requested during pregnancy. The letters T, R, C, H represent Toxoplasma, Rubella, cytomegalovirus, and Herpes. Being infected with any one of these during pregnancy could injure the fetus.

23. Mycology
Mycology is the study of fungi, a diverse group of microorganisms that exist in mold or yeast form. Most fungi are found in soil and on decaying plant matter. Of 250,000 known fungal species, only about 180 are considered capable of causing disease.
Infection caused by fungi is called mycosis. The mycosis incidence is related to the degree of exposure to fungi in living conditions, occupation, and leisure activities, and to immune status.
Most pathogenic fungi can infect any exposed individual. Two important examples are Histoplasma capsulatum and Coccidioides immitis. Others, such as Candida and Aspergillus, are opportunistic pathogens; they ordinarily cause disease only in immunosuppressed (compromised) patients, such as those with AIDS.

24. Characteristics of Molds
Molds have branching filaments called hyphae that make up the vegetative structure, the mycelium. They reproduce by forming spores. Most molds are aerobic and grow in the range of degree Celsius. They will grow on the usual bacteriological media; however, their growth is so slow that bacteria usually overgrow them. One of the best-known media to select for growth of pathogenic fungi is Sabouraud’s dextrose agar, which contains dextose, maltose, and peptones. In addition, antibiotics may be included to inhibit growth of bacteria and nonpathogenic fungi.

25. Characteristics of Yeast and Identifying Fungi
The most common is unicellular; one celled that is egg shape.
Yeasts reproduce by budding instead of forming spores.
350 known species of yeasts
Yeasts are used in fermentation.
Some yeast are useful for industrial purposes.
Some yeasts are pathogenic.
Yeasts grow best with an abundant supply of oxygen and grow satisfactorily on common bacteriological media.
EXAMPLES OF YEAST:
Candida usually known as C. albicans.
Malassezia furfur

26. Microbiology is the study of wide variety of organisms, some helpful to man and some harmful.
Diseases my cause microorganisms because of the discovery of antibiotics.
Microorganisms can undergo rapid genetic change.
Identification techniques for fungi depend on whether the organism is a mold or yeast.
Molds are largely identified by macroscopic and microscopic, study of their morphology and the spores the produce.
The Uni-Yeast-Tek system identifies yeasts based on their ability to ferment certain sugars.