Unit #5E – Clinical Unit #5E – Clinical Laboratory Testing – Laboratory Testing –

Basic Clinical Basic Clinical MicrobiologyMicrobiologyIncludes study of bacteria Includes study of bacteria

(bacteriology), parasites (parasitology), (bacteriology), parasites (parasitology), viruses (virology) and fungi (mycology)viruses (virology) and fungi (mycology)

Cecile Sanders, M.Ed., MLS(ASCP)Cecile Sanders, M.Ed., MLS(ASCP)

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology

– Bacteriology Bacteriology Study of a large diverse group of single Study of a large diverse group of single

celled prokaryote microorganisms which celled prokaryote microorganisms which multiply by fission to form a “colony” (on multiply by fission to form a “colony” (on solid media), which can be observed for solid media), which can be observed for characteristic appearance. characteristic appearance.

Bacteria cannot be seen with the naked Bacteria cannot be seen with the naked eye. They can only be seen after staining eye. They can only be seen after staining them with special dyes and observing them them with special dyes and observing them under a microscope.under a microscope.

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology– Bacterial Microscopic MorphologyBacterial Microscopic Morphology

Coccus - round (cocci = plural)Coccus - round (cocci = plural)– Example: Streps, staphs, NeisseriaExample: Streps, staphs, Neisseria

Diplococcus - cocci in pairs (diplococci = Diplococcus - cocci in pairs (diplococci = plural)plural)– ExampleExample: : Strep. pneumoniaeStrep. pneumoniae

Bacillus or rods - parallel sides (bacilli = Bacillus or rods - parallel sides (bacilli = plural)plural)– Example: Example: E. coliE. coli

Spirochetes - curved or spiral organismsSpirochetes - curved or spiral organisms– Example: Example: Treponema pallidumTreponema pallidum

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology– Cocci/DiplococciCocci/Diplococci

– Bacilli/Rods Bacilli/Rods

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology– Spirochetes Spirochetes

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology– Gram Stain Gram Stain

http://www.uphs.upenn.edu/bugdrug/antibiotic_manual/Gram3.htmhttp://www.uphs.upenn.edu/bugdrug/antibiotic_manual/Gram3.htm

Most bacteria fall into one of two Most bacteria fall into one of two categories:categories:– Gram-positive = microorganisms that stain purpleGram-positive = microorganisms that stain purple

- - Example: Streps, staphsExample: Streps, staphs– Gram-negative = microorganisms that stain pink Gram-negative = microorganisms that stain pink

or redor red - - Example: Example: E. coli, E. coli, NeisseriaNeisseria Purpose of Gram Stain: Provides valuable Purpose of Gram Stain: Provides valuable

information for physician to start antibiotic information for physician to start antibiotic therapy, as antibiotics act differently on therapy, as antibiotics act differently on gram (+) vs. gram (-) organismsgram (+) vs. gram (-) organisms

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology– Gram Positive Cocci Gram Positive Cocci

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology– Gram Positive BacilliGram Positive Bacilli

– Gram Negative Cocci Gram Negative Cocci

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology– Gram Negative Bacilli Gram Negative Bacilli

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology– Clinical Bacteriology TermsClinical Bacteriology Terms

Pathogens / pathogenic – capable of causing Pathogens / pathogenic – capable of causing disease disease

Communicable - capable of being transferred Communicable - capable of being transferred from one person to anotherfrom one person to another

Normal flora - natural micro-inhabitants of the Normal flora - natural micro-inhabitants of the bodybody

Opportunists / Opportunistic pathogens – Opportunists / Opportunistic pathogens – organisms that only cause disease in organisms that only cause disease in compromised individuals compromised individuals

Antibiotic susceptibility testing – tests for Antibiotic susceptibility testing – tests for sensitivity of organism against varioussensitivity of organism against various antibioticsantibiotics

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology Specimen collection - Body sites / Specimen collection - Body sites /

fluids cultured to grow fluids cultured to grow microorganismsmicroorganisms

– Fastidious organisms - require special Fastidious organisms - require special medium / conditions to growmedium / conditions to grow

– Aerobic - organisms which require Aerobic - organisms which require oxygen to grow or liveoxygen to grow or live

– Anaerobic - organisms which live and Anaerobic - organisms which live and grow only in absence of oxygen. grow only in absence of oxygen. http://www.shellab.com/bactron.htmlhttp://www.shellab.com/bactron.html

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology– Microbiological Safety Cabinets - H(igh) Microbiological Safety Cabinets - H(igh)

E(fficiency) P(article) A(ir filter) “HEPA”E(fficiency) P(article) A(ir filter) “HEPA”

Air moves away from worker, over specimen, Air moves away from worker, over specimen, through filter, and vented to outside through filter, and vented to outside http://www.terrauniversal.com/products/gloveboxes/http://www.terrauniversal.com/products/gloveboxes/accessories_gbx/filtrationmodules.phpaccessories_gbx/filtrationmodules.php

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology– Disinfectants - chemicals used on Disinfectants - chemicals used on

working areas to kill or control growth working areas to kill or control growth of organisms in their active or of organisms in their active or vegetative stages (NOT resting stages, vegetative stages (NOT resting stages, such as spores). Some harsh such as spores). Some harsh disinfectants will kill spores, toodisinfectants will kill spores, too EXAMPLE: 10% bleach, phenolsEXAMPLE: 10% bleach, phenols

– Antiseptics - chemicals used to control Antiseptics - chemicals used to control microorganisms on living tissuemicroorganisms on living tissue EXAMPLE: 70% isoprophyl alcohol, BetadineEXAMPLE: 70% isoprophyl alcohol, Betadine

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology– Sterilization - methods used to kill all Sterilization - methods used to kill all

organisms and their resting stagesorganisms and their resting stages EXAMPLE: AutoclavingEXAMPLE: Autoclaving

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology Processing of Specimens Processing of Specimens

– Agars - solid medium made of seaweed Agars - solid medium made of seaweed extract; bacteria grow on these agars extract; bacteria grow on these agars and appear as small to large dotsand appear as small to large dots Enrichment agars for growth – contain Enrichment agars for growth – contain

extra nutrients extra nutrients – Example: Blood AgarExample: Blood Agar

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiologyDifferential agars – differentiate organisms Differential agars – differentiate organisms

by color or growth patternby color or growth pattern– Example: MacConkey Agar – inhibits the Example: MacConkey Agar – inhibits the

growth of gram positive organisms while growth of gram positive organisms while allowing gram negative organisms to growallowing gram negative organisms to grow

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology Selective agars – Selective agars –

Inhibit the growth of Inhibit the growth of certain certain microorganisms microorganisms while allowing other while allowing other organisms to groworganisms to grow

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology Antibiotic Sensitivity (Susceptibility) Antibiotic Sensitivity (Susceptibility)

TestingTesting– Kirby-Bauer MethodKirby-Bauer Method

– MIC – Minimum Inhibitory MIC – Minimum Inhibitory Concentration – Provides information Concentration – Provides information on weakest dose of antibiotic that on weakest dose of antibiotic that would be effectivewould be effective

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology Parasitology –Parasitology –

– Common human parasites Common human parasites Enterobius vermicularis “Pin Worm”Enterobius vermicularis “Pin Worm” Giardia lambliaGiardia lamblia Trichomonas vaginalisTrichomonas vaginalis

– O & P (Ova and Parasites) - Detection O & P (Ova and Parasites) - Detection of Intestinal Parasitesof Intestinal Parasites Helminths - flatworms, round worms, Helminths - flatworms, round worms,

flukes, or hookwormsflukes, or hookworms Amoeba in cyst or trophozoite stageAmoeba in cyst or trophozoite stage

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiologyLife cycle of GiardiaLife cycle of Giardia

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiologyLife cycle of Ascaris (round worm)Life cycle of Ascaris (round worm)

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiologyLife cycle of amoebaLife cycle of amoeba

parasiteparasite

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiologyStool samples - usually collected X3 and at Stool samples - usually collected X3 and at

least 24 hours apartleast 24 hours apartMost common preservative = ParaPak (has Most common preservative = ParaPak (has

two vials, one with Polyvinyl Alcohol [PVA] two vials, one with Polyvinyl Alcohol [PVA] and the other with formalin)and the other with formalin)

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology““Wet Prep” for detection of Wet Prep” for detection of Trichomonas Trichomonas

vaginalisvaginalis

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology VirologyVirology

– CharacteristicsCharacteristics Intracellular parasitesIntracellular parasites Too small to be seen with light microscopyToo small to be seen with light microscopy Contain either DNA or RNA, but not bothContain either DNA or RNA, but not both

– Common viral infections include the Common viral infections include the common cold, influenza, measles, common cold, influenza, measles, chickenpox, hepatitis. Others viral chickenpox, hepatitis. Others viral infections include polio, HIV, bird flu, infections include polio, HIV, bird flu, West Nile virus.West Nile virus.

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology– Virus DetectionVirus Detection

Most detected by testing for specific Most detected by testing for specific antibodies (review #5C PowerPoint)antibodies (review #5C PowerPoint)

Some viruses can be culturedSome viruses can be cultured

– Anatomy of a virus particle – check Anatomy of a virus particle – check this website:this website:

http://www.nwabr.org/studentbiotech/winners/http://www.nwabr.org/studentbiotech/winners/studentwork/2006/WB_SC_Rimbakusumo/studentwork/2006/WB_SC_Rimbakusumo/wworks.htmlwworks.html

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology Mycology - study of fungus. Infection with Mycology - study of fungus. Infection with

fungus is called a fungus is called a mycosismycosis– Types of Specimens for Fungal CulturesTypes of Specimens for Fungal Cultures

Skin scrapingsSkin scrapings Nail clippingsNail clippings Scalp scrapingsScalp scrapings SputumSputum BloodBlood Bone marrowBone marrow Lung biopsiesLung biopsies

– Fungi (plural of fungus) are either “molds” or Fungi (plural of fungus) are either “molds” or “yeasts”“yeasts”

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology– Molds - filamentous fungiMolds - filamentous fungi

Assorted molds cultureAssorted molds culture

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiology– Yeasts - unicellularYeasts - unicellular

Usually egg-shaped Usually egg-shaped Reproduce with buds Reproduce with buds Pasty in appearance Pasty in appearance

Unit #5E – Clinical Laboratory Unit #5E – Clinical Laboratory Testing - Basic Clinical Testing - Basic Clinical

MicrobiologyMicrobiologyPhotos from clinical microbiology Photos from clinical microbiology

laboratories:laboratories: