Microbiology Flashcards
Organisms under Prokaryotes
Eubacteria
Cyanobacteria
Archaebacteria
DNA of Prokaryotes
Not enclosed within a membrane and usually a singular circularly arranged
Membrane-bound organelles of Prokaryotes
Absent
Main component of prokaryote CW
Polysaccharide peptidoglycan
Replication of prokaryotes
Binary fission
Only prokaryote/s without CW
Mycoplasma and Ureaplasma
Cytoplasmic membrane of prokaryotes
Fluid phospholipid bilayer WITHOUT CHO and sterol
Only prokaryote/s with CHO and/or sterol in their cytoplasmic mebrane
Mycoplasma and Ureaplasma (sterol)
Site of energy production in prokaryotes
Cytoplasmic membrane
Site of protein synthesis in prokaryote
Free ribosomes
Components of the peptidoglycan layer of prokaryotes
Chains of alternating N-acetyl-d-glucosamine and N-acetyl-d-muramic acid
Other term for the peptidoglycan layer
Murein layer
Structure special to Gram-positive bacteri
Teichoic Acid
Function of teichoic acid
Crystal violet-iodine-teichoic acid-Mg++ complex in insoluble to alcohol
Steps and reagents for Gram staining
1 stain: Crystal violet
Mordant: Gram’s iodine
Decolorizer: Acetone alcohol
2 stain: Safranin
Most critical step in Gram staining
Decolorization
General rule for gram staining: cocci
Gram positive except:
Neisseria
Brahamella
Veillonella
General rule for gram staining: bacilli
Gram negative except: /aerobic/ Bacillus Corynebacterium Erysipelotrix Listeria Mycobacterium Nocardia /anaerobic/ Actinomyces Clostridium Propionobacterium
Spore forming bacteria
Bacillus and Clostridium
Fungi-like bacteria:
Nocardia and Actinomyces
Bacteria seen in Blood film
Borrelia
Hot-staining AFS
Ziehl-Nelseen
Cold-staining AFS
Kinyoun
Steps and reagents for Ziehl-Neelsen Stain
1 stain: Carbol fuchsin
Mordant: Steam/heat
Decolorizer: Acid alcohol
2 stain: Methylene blue or malachite green
Preferred AFS for tissues
Kinyoun
Steps and reagents for Kinyoun Stain
1 stain: Carbol fuchsin
Mordant: Tergitol
2 stain: Acid alcohol
2 stain: Methylene blue or malachite green
Negative for AFS
Blue / Green
Positive for AFS
Red
Specific name for lipid inclusions; specify organism
Much granules; MTB
Specific name for polyphosphate inclusions; specify organism
Babes-Ernst/Metachromatic/Volutin granules; Corynebacterium
Stain for Babes-Ernst granules
Burke’s modified stain
Organism with bipolar bodies
Y. pestis
Stain for bipolar bodies
Wayson’s stain
Stain for spores
Shaeffer & Fulton
Dorner’s
Wirtz & Conklin
Composition of spores
Calcium dipicolinate / Dipicolinic acid
Test to differentiate spore-forming bacteria
/both are Gram-postive/
Bacillus: catalase + (aerobic)
Function of capsule
Increase virulence by preventing phagocytosis
Specific antigen for capsule
K antigen; Vi antigen for S. typhi
Composition of capsule
Continuous polysaccharide except for B. anthracis (polypeptide)
Capsular bacteria
H. influenze
N. meningitidis
S. pneumoniae
B. anthracis
Stains for capsule
Quelllung
Hiss
India Ink / Nigrosin
Bacteria with slime layer instead of capsule and causes prosthetic endocarditis
S. epidermidis
Synonymous to Fimbriae
Pili
Function of pili
Ordinary pili: attachment
Sex pili: conjugation
Atrichous
No flagellum
Monotrichous
Flagellum on one pole
Amphitrichous
Single lagellum at both poles
Lophotrichous
Tuft of flagellum on one or both poles
Peritrichous
Flagella all around the organism
All enterobactericae except Shigella and Klebsiella
Periplasmis flagella
Axial filaments
Found only in Spirochetes
Temperature for motility test
Room temp (25C)
Tests for Motility
Hanging Drop
Semisolid Medium (SIM)
Flagellar stains
Flagellar stains
Contain Tannic acid to precipitate and coat flagella
- Leifson
- Gray
- Fisher and Conn
Tumbling motility
Listeria
Darting motility
Campylobacter
Gliding motility
Capnocytophaga
Component of Mycobacteria that is hard to gram stain
Mycolic Acid
Source of endotoxin
Gram negative bacteria
Differentiate exotoxin and endotoxin : release
Exo: by living cells; metabolically produced
Endo: part of CW; released when CW is lysed
Differentiate exotoxin and endotoxin :heat stability
Exo: labile
Endo: stable
Differentiate exotoxin and endotoxin : immunologic
Exo: converted to toxoids; easily neutralized with anti-toxin
Differentiate exotoxin and endotoxin : Pharmacologic
Exo:
- cytotoxin: kills host cells
- enterotoxin: damage GIT cells
- neurotoxin: interferes with nerve impulses
Endo: non specific; fever, septic shock, DIC
Differentiate exotoxin and endotoxin : Toxicity
Exo: high
Endo: low
Test to detect endotoxin in body fluids and instruments
Limulus Lysaic Test
Reagent: blood of horseshoe cran
Positive result: clumping due to lysate
Fried rice pathogen
Bacillus cereus
Canned good pathogen
Clostridium botulinum
Pathogen in salad/coleslaw
Listeria
Most common pathogen causing food poisoning
Staphylococcus aureus
Obligate aerobes
Brucella, Bordetella, Francisella, Pseudomonas, Neisseria
Obligate anaerobe
Bacteroides, Clostridium
Facultative anaerobe
Staphylococcus, Streptococcus
Microaerophilic
Campylobacter (5% O2 10%CO2 85%N)
Capnophilic
/HACEK/ Haemophilus Actinobacillus Cardiobacterium Einella Kingella
Stain/Test for anaerobes
Methylene blue
Negative: colorless colonies
Candle Jar is used to…
increase CO2 concentration
Temperature ranges for bacteria
Psychrophillic: less than 10C
Mesophillic: 20-40C
Thermophillic: 30-37C
pH ranges for growth of bacteria
Acidophile: pH 3
Alkaline: pH 8-10 (Vibrio)
Clinically relevant: 6.5-7.5
Describe each stage of the growth cycle of bacteria
Lag phase: little to no multiplication; adjustment period
Log phase: max multiplication; active metabolism
Stationary phase: growth = death; exhaustion of nutrients and buildup of toxins
Decline phase: increase in death; increase in toxins; low nutrients; unfavorable pH
Tissue media for Chlamydia culture
McCoy cells
Tissue media for viruses
Chick embryo, Vero cells
Tissue media from African green monkey
Vero cells
Tissue media from lung carcinoma
A549 cells
Tissue media from cervical carcinoma
HeLa cells
- Henrietta Lacks
Tissue media from laryngeal carcinoma
Hep2 cells
Culture media for most non-fastidious bacteria
Simple/General isolation/General purpose media
- nutrient agar/broth
- trypticase soy agar/broth
Culture media with nutrient supplementation
Enriched media
- BAP
- CAP
Culture media for enhance growth of specific bacteria
Enrichment media
- Selenite and tetrathionate broth : Salmonella and Shigella
- Alkaline Peptone Water: Vibrio
Culture media to select the growth of a particular organism and inhibit the growth of others
Selective media
Inhibitors for Gram positive bacteria
Dyes: - Gentian violet - Crystal violet Bile salt: - Sodium desoxycholate
Inhibitors for Gram negative bacteria
Sodium azide
Potassium tellurite
Phenylethyl alcohol
Selective culture medium for MTB
Lowenstein-Jensen; Petragrani
Inhibitor: malachite green
Selective culture medium for C. diptheriae
Mueller tellurite
Inhibitor: potassium tellurite
Selective culture medium for N. gonorrhoeae
CAP with antibiotics
- Thayer Martin = vancomycin + colistin + nystatin
- Modified Thayer Martin = vancomycin + colistin + nystatin + trimethropim
- Martin Lewis = vancomycin + colistin + anisomycin + trimethoprim
- New York City Agar = vancomycin + colistin + amphotericin B + trimetoprim
Selective differential medium for Staphylococcus sp.
Mannitol Salt Agar
- 7.5% NaCl
- Mannitol
- phenol red
MF: yellow colonies = S. aureus
NMF: pink colonies = S. epidermidis, S. saprophyticus
Selective differential media for Vibrio sp.
Thiosulfate Citrate Bile Salt
- Sucrose
- Bromthymol blue (A: yellow; K: green)
SF: yellow
NSF: green
Rapid lactose fermenters of Enterobacteriaceae
/EKE/
E. coli
Klebsiella
Enterobacter
– postive for lactose permease
Late lactose fermenters of Enterobacteriaceae
/SSSCHY/ Serratia Salmonella arizonae Shigella sonici Hafnia Yersinia Citrobacter
– positive for OMPG
Non-lactose fermenters of Enterobacteriaceae
/EEMPPSS/ Edwardseialla Erwinia Morganella Proteus Providencia Salmonella Shigella
Eosin-Methylene Blue Agar
Lactose
LF: Pink to purple
NF: colorless
E. coli: pink colonies with green sheen
Klebsiella: pink mucoid colonies
Enterobacter: pink colonies with dark center (fish eye)
MacConkey Agar
Lactose
Crystal violet, Bile salt
Neutral red (A: red; K: colorless)
LF: pink colonies
NLF: colorless
Hektoen Enteric Agar
Lactose, sucrose, salicin
Bile salt
Bromthymol blue (A: yellow; K: blue)
Ferric ammonium sulfate
/SPACEd/: Green/colorless medium with black
- Salmonella, Proteus, Arizon, Citrobacter, Edwardsiella
Salmonella Shigella Agar
Lactose
Neutral red (A: red; K: colorless)
Ferric citrate
Salmonella: colorless colonies with black
Shigella: colorless colonies without black
Bile Esculin Agar
Group D enterococci
Bordet-Gengou agar
Isolation of B. pertussis (mercury droplet)
Potato-glycerol-based with defibrinated blood and methicillin
Buffered charcoal-yeast extract agar
Enrichment for Legionella spp.
CIN
Selective for Yersinia spp.
Cefsulodin, irgasan, novobiocin
Regain Lowe
Enrichment and selective medium for B. pertussis
Preferred isolation of B. pertussis
Regan Lowe
Skirrow Agar
Campylobacter (42-43C) and Helicobacter (35-37C)
Todd-Hewitt broth with antibiotics
Selective and enrichment for S. agalactiae
Human blood bilayer tween medium
G. vaginalis
Transport media for N. gonorrhea
Transgrow
Medium for susceptibility testing
Mueller-Hilton Agar
Depth: 4mm
pH: 7.2-7.4
24mm disk distance
Media for biochemical testing
TSI, LIA
Triple Sugar Iron Agar
Lactose, Sucrose, Glucose Phenol Red (A: yellow; K: red) Ferrous sulfate (black)
Slant: LF and SF
Butt: GF, gas, H2S
All eterobacteriaceae are gas producers in TSI except
Shigella
Lysine Iron Agar
Glucose, lysine
Slant: Lysine deamination (+ red - purple)
Butt: Lysine decarboxylase (+ purple - yellow)
Lysine carboxylase positive
Salmonella
Lysine deaminase positive
Proteus
Providencia
Morganella
Min. Inhibitory Concentration
Minimum concentration that inhibits bacterial growth
Min. Bactericidal Concentration
Lowest concentration that kills bacteria
Disk diffusion / Susceptibility testing
Kirby bauer
Mueller-Hilton Agar
Causes increased resistance of P. aeruginosa to aminogycosides and decreased activity of tetracyclines to all organisms
Excessive Mg++ and Ca++
E-test
Susceptibility testing using plastic test strips with antimicrobial concentration gradient
Automated susceptibility testing
Measures optical density using Vitek systems and validated by Advanced Expert System (AES) software
Antimicrobial agents that interfere with CW synthesis
Beta-lactams (penicillin)
Bacitracin
Cycloserine
Glycopeptides
Antimicrobial agents that interfere with Protein synthesis
Aminoglycosides (-mycin, -micin)
Tetracycline (inhibit bone growth)
Chloramphenicol (last resort! causes aplastic anemia)
Antimicrobial agents that interfere with Nucleic Acid synthesis
Sulfonamides (inhibit folic acid)
Rifampicin (causes orange-red secretions)
Antimicrobial agents that interfere with cell membrane function
Polymyxin
Antimicrobial agents that interfere with fungi
Amphotericine B, nystatin, anisomycin
Sterilization vs Disinfection vs Antiseptic
Sterilization: kills ALL forms of microbial life
Disinfection: destroy all pathologic organisms but not necessarily all organisms
Antiseptic: Microbiostatic agents used on living tissues
Most effective method of sterilization
Autoclave
Specifics for autoclave (media and instruments)
121C at 15lbs psi for 15mins
Specifics for autoclave (medical waste)
132C for 30-60mins
Quality control for autoclave
Spores of Bacillus stearothermophilus
Types of fractional sterilization
a. Tyndallization
b. Inspissation
Flowing steam 100C for 30mins for 3 days
Tyndallization
75-80C for 3 hours for 3 days
Inspissation
Alternate heating, incubation, heating
Fractional sterilization
For sterilization of inoculating loops and needles
Flame
Oven for sterilization - temp and time
160-180C for 90-120min
Quality control for oven
Spores of Bacillus subtilis
Most common method for treating infectious waste;
870-980C
Incinaration
98% effective filter
Asbestos filter
100% bacterial sterility
0.22 micrometer
Membrane filter
Filtration of air
High-efficiency particulate filters
0.2 micrometer
Sterilizing plastic syringes, catheters, or gloves
Ionizing radion
Gamma rays = short wavelength, high energy
Most common chemical sterilant
Cold sterilization
For materials that cannot be autoclaved
Ethylene oxide
Sterilize HEPA filters in BSCs
Formaldehyde vapor and vapor phase hydrogen perocide
Sporicidal
Does not corrode lenses, metal, or rubber
Cold sterilization
Glutaraldehyde
Effective in the presence of organic material
Cold sterilization
Peracetic acid
Boiling as disinfectant
100C for 15mins
Disinfectant to eliminate food-borne pathogens
Pasteurization
Pasteurization at 63C for 30 mins
Batch Method
Pasteurization at 72C for 15 mins
Flash Method
Long wavelength, low energy
Non-ionizing radiation
e.g. mercury lamps
Phenol, phenolics, QUATs, chlorine, 2% aqueous glutaraldehyde
Disinfectant
Alcohol, tincture iodine, iodophor
Antiseptic
Why is 70% ethyl alcohol more effective than 95%?
Water hydrolizing bonds in protein molecules make the killing more effective
Can be used as a disinfectant to kill endospores but toxic to humans
Aldehydes: formaldehyde, glutaraldehyde
Iodine or chlorine disinfectant
Halogens
Composition of iodophor
Iodine + detergent
Neutralize chlorine with…
sodium thosulfate
Examples of heavy metals as disinfectants
Hg: merthiolate; antiseptic, antifungal
Cu: Algicide
Ag(NO3): Credes prophylaxis
Expression of the bactericidal power of a particular substance as compared to pure phenol
Phenol coefficient = highest dilution of sample needed / highest dilution of phenol needed
Quality control for ionizing radiation
Bacillus pumilis
Quality control for ethylene oxide
Bacillus sibtilis var. globii
BSC: open front, negative pressure, sterilize air going out
BSC Class 1
BSC: sterilize air going in and out; also known as LAMINAR FLOW BSC
BSC Class 2
BSC: system is entirely clode; air entering and leaving is sterilized by HEPA filter
BSC Class 3
Airflow patter of BSC Class 1
Enter front –> rear –> top –> through HEPA filter
Airflow patter of BSC Class 2-A
70% recirculated through HEPA
vExhaust via HEPA
Airflow patter of BSC Class 2-B1
30% recirculated through HEPA
Exhaust via HEPA and hard-ducted
Airflow patter of BSC Class 2-B2
No recirculation
Total exhaust via HEPA and hard-ducted
Airflow patter of BSC Class 2-B3
Same with Class 2-B2 but under negative pressure
Exhaust air is ducted
Airflow patter of BSC Class 3
Supply air inlets through 2 HEPA filters
Examples of critical values in microbiology
- positive blood culture
- postive CNS gram stain or culture
- postive cryptococcal antigen test or culture
- postive blood smear for malaria
- S. pyogenes from a sterile site
- MTB culture positive
- S. agalactiae or herpes simplex virus from genital site of pregnant woman
Signs of growth in blood culture
Turbidity
Clot
Hemolysis
Bubbles
Additive in blood culture media set
SPS 0.025% (yellow top)
- prevents phagocytosis
- neutralizes bactericidal effect of blood serum (complement)
When patient is on antimicrobials
use thiol broth or antimicrobial removal device
Culture for throat and nasopharyngeal specimen
Todd-Hewitt broth - fluorescence mincroscopy of Beta Strep
Most abundant normal flora of throat
Alpha-hemolytic strep: Viridans
Most common pathogen in throat
Group-A strep: S. pyogenes
Culture for H. influenza nasopharyngeal swab
BAP or CAP with S. aureus streak
Culture for N. meningitidis nasopharyngeal swab
enriched BAP
Culture for B. pertussis nasopharyngeal
Charcoal cephalexin medium (Regan Lowe)
Bartelette’s critieria
For sputum specimen
< 10 epithelial cells / LPF = high saliva content
> 25 /LPF = pathologic
Additive for urine
Boric acid
Collection for urine
a. Midstream clean-catch
b. Catheterized urine
c. Suprapubic urine – anaerobic culture
Most common agent of UTI
E. coli > 100000 CFU / mL
Factors for callibrated loop for urine specimens
1 microliter loop x 1000
10 microliter loop x 100
Culture for genital specimens
McCoy’s media
How many tubes/collections for CSF?
1: chem and sero
2: micro : most important
3: hema and physical
Causative agent for meningitis for neonatal
Group B step and Gram negative rods
- S. agalactiae
Causative agent for meningitis for under 5
H. influenza
Causative agent for meningitis for for 5-29
N. meningitidis
Causative agent for meningitis for 30 up
S. pneumoniae
Temp storage for CSF
37C
Temp storage for urine, stool, swab, sputum
4C
Serum
-20C for 1 week
Tissues or specimens for long-term storage
-70C
Staphylococcus vs Micrococcus : morphology
Staph: in clusters
Micro: in tetrads/sarcinae
Describe Alpha hemolysis
- Incomplete / partial lysis of RBCs around the colony
- Greenish discoloration around colony
Describe Beta hemolysis
- Complete lysis of RBCs around the colony
- Clear area around the colony
Describe Gamma hemolysis
- No lysis of RBCs
Describe Alpha-Prime hemolysis
- Small zone of alpha hemolysis surrounded by a zone of beta hemolysis
- Occurs after refrigeration
Differentiate growth of Staph spp. in Loeffler’s Serum Slant
S. aureus: golden yellow
S. citreus: lemon yellow
S. epidermidis: white
Only Mannitol-Fermenter Staphylococcus species
S. aureus
Medium for mannose fermentation
Mannitol Salt Agar (MSA)
Positive result for Catalase test
Effervescence / Bubbles
Staph vs Strep: Catalase test
Staph: +
Strep: -
Staphylococcus vs Micrococcus : Lysotaphin
Staph: S
Micro: R
Staphylococcus vs Micrococcus : Bacitracin
Staph: R
Micro: S
Staphylococcus vs Micrococcus : Modified oxidase
Staph: -
Micro: +
Staphylococcus vs Micrococcus : Glucose utilization
Staph: fermenter
Micro: Oxidizer
Positive result for Modified Oxidase test
Blue
CHO Oxidation Fermentation Test : indicator
Bromthymol blue
- positive: yellow
Most important pathogenic determinant of S. aureus
Coagulase
Slide coagulase: detects, reagent, positive result
- Detects coagulase factor
- EDTA > Citrate
- Clumping
Tube coagulase: detects, reagent, positive result
- Detects free coagulase
- Rabbit’s plasma
- gel-like fibrin clot
DNAse test : medium
DNA with methyl green
- positive result is clearing of medium
- : S. aureus, Moraxella, Serratia
S. epidermidis vs S. saprophyticus: Novobiocin
S. epidermidis: S (16mm)
S. saprophyticus: R
Pathologic determinants of S. aureus
- inhibits phagocytosis
Protein A
Pathologic determinants of S. aureus
- converts fibrinogen to fibrin; may coat neutrophils with fibrin to prevent phagocytosis
Coagulase
Pathologic determinants of S. aureus
- associated with initiation of skin infections
Lipase
Pathologic determinants of S. aureus
- aka spreading factor
Hyaluronidase
Pathologic determinants of S. aureus
- degrades DNA
DNAse
Pathologic determinants of S. aureus
- associated with staphylococcal scalded skin syndrone
Exfoliatins
Pathologic determinants of S. aureus
- lysis of neutrophils and macrophages
Leukocidins
Pathologic determinants of S. aureus
- lyse erythrocytes
Hemolysins
Pathologic determinants of S. aureus
- associated with food poisoning and TSS
Enterotoxins
Drug of choice for serious staphylococcal infections
Vancomycin
Gold standard for MRSA detection
mecA gene
- by molecular NA probes
- PRC amplification
Lancefield Group A : species
S. pyogenes
Lancefield Group B : species
S. agalactiae
Lancefield Group C : patho
Pneumobia, cellulitis, abscess
Lancefield Group D: species
S. bovis
S. equinus
Lancefield Group A : patho
URTI
Scarlet fever
Erysipelas
Impetigo
Lancefield Group B: patho
Neonatal infections
Lancefield Group D : patho
UTI
Would infections
Lancefield Group D subgroup resistant to penicillin
Enterococci
Brown’s classification of Streptococcus spp is based on what?
Hemolysis pattern
Strep spp. with alpha hemolysis
- S. pneumoniae
- Viridans
- Some Group D
Strep spp with beta hemolysis
- Group A, B, C, some D
Strep spp with gamma
Most Group D
Hemolysins produced by Streptococcus spp.
Streptolysin S
- non-antigenic
- surface hemolysis
Streptolysin O
- antigenic
- sub-surface hemolysis
Organism with lancet flame, bullet-shaped diplococci morphology
S. pneumoniae
Growth of Streptococcus spp. on BAP
Pinpoint colonies with hemolytic patterns