Professional Documents
Culture Documents
Definition of Terms:
Anaerobic no oxygen Culture-plant
Aerobic- with oxygen Fastidious not easily grow
Aerosol- air transmitted Gram stain test for the presence of
Agar- extract from seaweed(liquid bacteria
when heated, solid when cold) Gram positive blue/purple
Bacilli- rod-shaped Gram negative - red
Cocci- spherical Hemolytic
Colony- group from one kind Inoculation - plant
Mordant chemical that increases the
affinity of the stain
HISTORY
Robert Hooke father of cytology
Anton Van Leeuwenhoek father of microbiology
Linnaeus - nomenclature
Jenner-vaccine
Robert Koch- Germ theory
Louis Pasteur- disproved abiogenesis
Elie Mechnikoff- phagocyotosis
Watson and Crick-DNA
METABOLIC CHARACTERISTICS
1. Oxygen H202, O2-
ENZYMES : Catalase 2H2O2 2H2O+ O2
Peroxidase 2H2O2 2H2O+ O2
Superoxide dismutase (SOD) 2H+ + 40- 2H2O2
2. Carbon Source
Phototrophs light
Chemotroph organic
Autotroph inorganic source
Heterotroph organic, glucose
Chemoheterotroph requires glucose, lipid, protein
Capnophilic - 10% CO2 required
Halophilic requires salt, salt-loving
NaCl (0.85%) human
1-3% - vibrio
6.5% - enterococcus
7.5% - staphylococci
3. Temperature
Psychrolic - cold, 2-10 oC, bacteria: Listeria, Yersinia
Mesophilic moderate, 20-40 oC (RT= 20-30 oC), most clinically important
Thermophilic - heat
Hyperthermophilic extreme temperature
e.g. bacteria: Bacillus stearothermophilus, Bacillus Subtilis
Other:
42oC Campylobacter
5oC Listeria
35-37oC
4. Hemolytic Pattern
Alpha partial hemolytic, green
Beta clearing of colony
Gamma no hemolysis
Alpha-prime Alpha+Beta
5. pH requirement
acidophile 3.0-6.5 pH, bacteria: Lactobacillus Lactonica lactis
alkalophile 8-10 pH, bacteria: Vibrio
neutral/slightly alkaline (7.35-7.45), optimum
GRAM STAIN
1. Gram positive blue/purple
2. Gram negative red
Exception:
Mycobacteria
Spirochetes
Mycoplasma
BACTERIAL STRUCTURE
1. Cell Wall (Peptidoglycan)
Techoic Acid - the affinity of the stain, G(+), crystal violet
2. Outer membrane Gram (-) rich in lipid
3. Lipopolysachharide (LPS) Gram Negative ( virulence)
Endotoxin dead
4. Periplasmic Space Gram negative, resistance,
bacteria: Lactobacilllus (Lactamase) resistance
5. Capsule protects from phagocytosis, covers antigen of bacteria,
bacteria: Neisseria meningitidis cause meningitis
6. Cell membrane energy production, cytochrome electron transport, polymoxin
7. Ribosome repair, site of protein synthesis, erythromycin
8. Plasmid nonchromosomal DNA, carries resistant gene
9. Pili/Fimbriae 2 functions:
Attachment e.g. E.Coli
Conjugation
Flagella
a. Atrichous w/out flagella
b. Monotrichous vibrio
c. Apmhitrichous both ends
d. Lopotrichous tuft of flagella
e. Petrichous surrounded by flagella
10. Endospore dormant/nonvegetation, resilient
11. Toxin
Endotoxin Gram(-), DEAD
Exotoxin gram(-)/gram(+), ALIVE, exaletanus plasmin, e.g. Botulinum flaccid
Enterotoxin holds NaCl
BACTERIAL METABOLISM
Respiration w/ O2
Krebs Cycle
ETC (Elecrone
Glucose-CO2 and H2O
Oxidation w/ O2 Gluc-acid
Fermentation w/o O2
EMP(Embden Meyerhof Pathway)
Gluc-acid/alcohol
BACTERIAL GENETICS
Genotype genetic makeup/complete genome
Phenotype expressed(G+/G-)/observable
Plasmid extrachromosomal DNA
Transposon jumping genes w/n plasmid
Mutations change in nucleotide sequence
a. Point mutation one
b. Frameshift mutation more than one
DNA TRANSFER same objective but different mechanism
Transformation naked DNA
Transduction phages, mediated by bacteria infected by virus (bacteriophages)
Conjugation direct transfer through pili
BACTERIAL CONTROL
Sterilization all include spores, kills all forms of life
Disinfection pathogenic/flora
a. Disinfectant living, e.g. NaOCL (Hypo) 1:10
b. Antiseptics non-living, e.g. Alcohol
KILLING DEPENDS ON:
Type
Number
Chemical concentration e.g. NaOCl (1:10)
Duration of contact
Alcohol(1 min)
HIV (2 min)
HBV (10 min)
Organic matter/oil present
KILLING DEPENDS ON:
Mycolic acid acid and lipid in Mycobacterium Tuberculosis, refers to mycobacterium
Spores/dormant
Vegetative bacterial feeding stage, easy to kill
Enveloped virus unstable , note used to be exposed
Naked virus more resistant t
Chitin Fungi
LEVEL OF DISINFECTION/STERILIZATION
High sporicidal(kills the spores), tubercolocidal
Intermediate Tuberculocidal, NOT spores. e.g. Boiling
Low NOT sporicidal nor tuberculocidal. e.g. Alcohol
METHODS OF DISINFECTION AND STERILIZATION
1. Physical
Incineration dry heat, highest temp
waste disposal (870-980C)
Dry Heat Oven 160-180C / 1.5-3hrs. For glasswares
Cremation Disease control
Flaming needle/culture
Autoclave moist heat/steam under pressure. For media
15psi/121C/15-20mins
Boiling 100C/15-30mins (MTB)
Pasteurization 63C/30mins or 72C/15secs for milk
2. Filtration 100% sterility, thin membrane filters(0.22-0.45u cellulose nitrate) or cellulose
diacetate(.015-12u) for vaccines and antiobiotic
3. Chemical methods- mostly disinfectant
Formaldehyde/glutaraldehyde cold sterilant
Alcohol disinfectant (70%)
Phenol standard disinfectant/cell membrane
Zephiran (Bezalkonium Cl) use for Alcohol measurement of blood
Iodine halogen
NaOCl Hypo/Chlorox
OTHER DISINFECTANTS
Freezing
Lyophilization best for culture preservation/years
UVL pyrimidine/DNA, use in biosafety cabinet, targets DNA
H2O2 agua oxinada
Detergents cell membrane
SPECIMEN COLLECTION
Collected during acute phase/before treatment
Written order/site Sterile/non-sterile, aerobic or anaerobic
Culture/usual flora
Compared with diagnosis
ACID-FAST STAIN
Differentiate AFO(Acid Fast Organism) from NAFO (Non-acid Fast Organism)
Mycolic Acid resists acid decolorization
Brightfield Fluorescence
Method Ziehl-Neelsen Kinyoun Auramine-Rhodamine
(C-A-M) (C-A-M)
1 Stain Carbol-Fuchsin (red) Carbol-Fuchsin Auramine-Rhodamine
Mordant Heat Phenol (increased
detergent)
Decolorizer 3% acid alcohol 3% acid alcohol 0.5% acid alcohol
2 Methylene Blue Malachite Green 0.5% KMnO4 quenching
Result AFO-red AFO-red AFO yellow fluorescence
NAFO - Blue NAFO - Blue NAFO No fluorescence
UNIVERSAL PRECAUTIONS
Barrier protection gloves, masks, lab gown, puncture resistant biohazard container(color)
Color coding for waste category:
Black non-infectious dry waste
Green non-infectious wet waste
Yellow infectious and pathological waste
Yellow with black band chemical waste
Red sharp and pressurized containers
Engineering controls protects while working(BSC) from aerosols
Heat
UV
HEPA (High efficiency particulate air) removes 0.3 um particle
CULTURE MEDIA
Media contains nutrients for growth, isolation and ID, can be classified based on:
Physical State/Consistency
Solid 1.5% agar added
Semi-Solid 0.5-1% agar
Liquid no agar
Agar polysaccharide extract from seaweed/algae
Composition
Synthetic/commercial exact composition is known
Non-synthetic not exact/serum or blood/meat extract broth
Tissue culture living tissues/ immortal cells(cancer cells)
Chick embryo/eggs
A549 from lung cancer
Hela cell cervical cancer
Hep 2 cells laryngeal cancer
Dispensing/Distribution
Plated dispensed on sterile petri dish(EMB, Mac, BAP)
Preparation: Weigh Dissolve Autoclave Dispense
Tube on sterile tubes
Preparation: Weigh Dissolve Dispense Autoclave
Broth
Agar slant
Slant and butt
Butt
Use
Non-selective (CAP/BAP)
Selective inhibitory agents that does not affect the desired org. (stool)
Differential characteristics on medium(BAP)
Enriched for fastidious organism / CAP
Selective enrichment/broth media supports small numbers
Transport prevents replication
ROUTINE CULTURE MEDIA
BAP(Blood Agar Plate) fastidious/hemolysis/defibrinated blood(V factor)
CAP(Chocolate Agar Plate) Haemophilus/Neisseria/Isovitalex(X and V factors)
Thayer-Martin Agar(TMA) Modified chocolate/antibiotics added
Bacteria:
N. gonorrhoeae
N. meningitidis
Antibiotics:
Vancomycin G(+)
Colistin G(-)
Nystatin fungi (yeast)
Modified TMA added trimethoprim(proteus inhibitor)
Martin Lewis agar Neisseria / anisomycin in place of colistin
Eosin Methylene blue lactose fermentation
E and M indicators/ M inhibits G+
Mac Conkey same use w/ EMB
Bile salts and CV inhibits G+/ Neutral red (indicator)
Mannitol Salt agar(MSA) G+ isolation/ CPS not CNS
7.5% NaCl/Phenol red indicator
Phenyl Alcohol agar G+ isolation/PE inhibits G-
Selenite Broth - S and S/ Na hydrogen selenite inhibits most enterics
Xylose lysine desoxycholate - S and S/high NaCl inhibits enterics
Thioglycolate aerobes and anaerobes
ANAEROBIC CULTURE SYSTEM
Resazurin white(reduced) to pink(+)/used in PRAS
Methylene blue blue to white/pink(+)
Catalyst Palladium
Methods
Anaerobic jar 5-10% CO2
Prereduced anaerobically sterilized system (PRAS)
Anaerobic glove box
METHOD ENVIRONMENT
Aerobic Culture O2 21%
CO2 0.03%
Candle Jar O2 15%
CO2 5-10%
Anaerobic Jar O2 0%
CO2 5-10%
H2 5-10%
N2 80-90%
INOCULATION TECHNIQUES
Streaking accurate colony count. 2 purposes:
Quantitative
Isolated Colony
Semi Quantitative dilution streaks: yields isolates from pure colony
Key Characteristics presumptive Dx, reduces cost, QC on automation
Colony size (staph,strep,fungi)
Pigments
Staph (gold) Serratia (red)
Pseudomonas (green-yellow) Salmonella (Dark/Black)
E. coli ( ) TSI (yellow)
Shape/surface appearance (proteus,Kleibsiella)
Hemolysis
Odor pseudo (grapelike)
ANTIMICROBIAL THERAPY
Antibiotic chemical
Antimicrobial therapy use to treat Disease
(-cidal) kill
(- static) inhibits growth
Synergistic (1+1=3)
Antagonism ( 2 + 1 = 1)
Additive (1+1=2)
Indifference (A + B =A)
Broad spectrum Both G(+)/G(-) ; e.g. Tetracyclin
Narrow Spectrum either G (-) / G (+)
S Sensitive I Intermediate R Resistant
STREPTOCOCCI
GAMMA-HEMOLYTIC BACTERIA
Group D
Enterococcus: E. Faecalis
Test:
Bile Esculin (+) Black color result; reagent Oxgall (Bile Salts)
6.5% NaCl (+) turbidity result / yellow color
PYR (+) Red color result; reagent P-dimethylamino-cinnamaldehyde
Non-enterococcus: S. Bovis
Test:
Bile Esculin (+) Black color result; reagent Oxgall (Bile Salts)
6.5% NaCl (-) clear result/ no growth / no color change
PYR (-) yellow/orange color result ; reagent P-dimethylamino-cinnamaldehyde
Note:
Nutrionally Variant Stretococci (NVS)
Abiotrophia without life, needed vitamin B6 to grow
BACTERIAL TESTS
1. Gram Staining differentiate bacteria into two large groups
Reagent:
1o stain Crystal Violet
Mordant Iodine
Decolorizer acetone alcohol
Counter stain Safranin
Result:
Positive purple
Negative red
2. Catalase Test differentiate Staphylococcus from Streptococcus
Reagent
H202 Hydrogen Peroxide
Result
Positive bubbling reaction; bacteria Staphyloccus / Micrococcus
Negative no bubbling reaction; bacteria Streptococcus
3. Modified Oxidation differentiate Staphylococcus from Micrococcus
Result:
Positive Micrococcus
Negative Stapylococcus
4. Coagulase Test differentiate S. Aureus from Catalase Negative Staphlylococcus
Reagent:
Rabbit plasma/Human plasma
Slide Coagulase Test clumping factor
Result:
Positive clumping cocci; bacteria S. Aureus
Negative no clumping; bacteria S. Epidermidis / S. Saprophyticus
Tube Coagulase Test coagulation factor
Result:
Positive coagulate; bacteria S. Aureus
Negative no coagulation; bacteria S. Epidermidis / S. Saprophyticus
5. Novobiocin differentiate S. Epidermidis from S. Saprophyticus
Reagent:
Novobiocin (Zone of Inhibition = 16mm)
Result:
Sensitive S. Epidermidis
Resistant S. Saprophyticus
6. Hemolysis used to classify streptococci species
Reagent:
Blood Agar Plate
Result:
Alpha partial hemolysis / green; bacteria S.Pneumoniae and S. Viridans(2)
Beta complete hemolysis / yellow ; bacteria S. Pyogenes and S.Agalactiae and
other Lancefield Groups
Gamma no hemolysis/unchanged; bacteria Group D Streptococcus: E. Faecalis
and S. Bovis
7. Bacitracin(TAXO A) differentiate S. Pyogenes and Group B Streptoccus: S. Agalactiae
Reagent:
Bacitracin (No Zone of Inhibition)
Result
Sensitive S. Pyogenes
Resistant S. Agalactiae
8. CAMP Test differentiate Group B Streptococcus: S. Agalactiae from other Lancefield group
Named after 3 researchers who discovered ( Christie, Atkins, Munch-Petersen )
Reagent:
Cyclic adenosine monophosphate
Result:
Positive arrowhead; bacteria Group B: S. Agalactiae
Negative absence of arrow head; bacteria other Lancefield groups
9. Bile Solubility Test identify S. Pneumoniae from bile-insoluble Streptococci
Reagent:
10% Desoxycholate (BAP)
2% Desoxycholate (Tube)
Result:
Positive clearing of turbidity; bacteria S. Pneumoniae
Negative no clearing of turbidity; bacteria bile-insoluble Streptococi
10. Optochin Test (TAXO P) - identify S. Pneumoniae from Optochin-resistant Streptococci
Reagent:
Optochin (Zone of Inhibition 14mm)
Result:
Sensitive S. Pneumoniae
Resistant Optochin-resistant Streptococci
11. Bile Esculin Test identify Group D Streptococcus from other Streptococci
Reagent:
Oxgall (bile salts)
Result:
Positive black color; bacteria Enterococcus: E. Faecalis/Nonenterococcus: S. Bovis
Negative no black color form; bacteria other Streptococci
12. 6.5% NaCl Test - differentiate Enterococcus from Non-Enter.
Reagent:
Sodium Chloride
Result:
Positive turbidity / yellow color; bacteria Enterococcus: E. Faecalis
Negative no turbidity / no color change; bacteria Non-enterococcus: S. Bovis
13. PYR (Pyrrolidonyl Arylamidase) Test presumptive identification of group A Beta-Hemolytic
Streptococci and differentiate Enterococcus: E. Faecalis and Non-Enterococcus: S. Bovis
Reagent:
P-dimethylamino-cinnamaldehyde
Result:
Positive color red; bacteria S. Pyogenes and Enterococcus: E. Faecalis
Negative yellow/orange color; bacteria Non-Enterococcus: S. Bovis
14. Hippurate Hydrolysis Test presumptive identification Group B streptococci: S. Agalactiae
Reagent:
Sodium Hippurate
Ninhydrin Reagent
Result:
Positive purple/violet color; bacteria S. Agalactiae
Negative no color change; bacteria S. Pyogenes
END