General Principles Of Microbiology And Laboratory Methods Of Identification Flashcards
What should be considered when choosing an ATB
- Severity or degree of risk
- Broad coverage with empiric antibiotics
- Timing
- Source control
- True infection bc colonization
- Antimicrobial resistance
How does severity or degree of risk guide us when choosing an ATB
- Aggressive Vs non aggressive
- Emergent vs non-emergent
How does broad coverage with empiric ATBs guide us when choosing an ATB
- Starting an ATB with board coverage in a timely manner can be lifesaving
*selecting the wrong dose, improper route, or delay treatment can increase morbidity and mortality
How does timing guide us when choosing an ATB
- Cultures and specimens should be obtained before ATB, when possible
*should not be delayed in life-threatening infection
How does source control guide us when choosing an ATB
- Drain collection of pus when possible
What are the signs of a true infection
- Almost accompanied by inflammation
- Neutrophils present
What are signs of contamination/colonization
- Large number of epithelial cells
- Growth of normal skin flora
*improper specimen collection
What is MIC
- Minimal inhibitory concentration
*lowest concentration of Antimicrobial agent (drug) that will inhibit the growth of the microorganisms
Do you want a low MIC or high MIC
Low
*also request a C&S
What does a low MIC mean on a culture
There will be a larger zone of inhibition
*small amount of drug goes a long way to kill the organism
What does a high MIC mean on a culture
There will be a smaller zone of inhibition
*a lot of a certain drug is needed to kill the organism
What is susceptible
Microorganisms is inhibited by a concentration of antibiotic and can be appropriately treated with that drug
What is intermediate Antimicrobial susceptibility
The ATB may be effective in high doses
What is a resistant Antimicrobial
Microorganisms is not inhibited by the antibiotic
*cant treat with that drug
What are some of the resistant microorganisms
- MRSA (methicillin resistant staph aureus)
- VRE (vancomycin resistant enterococcus)
What are some ways to diagnose infectious diseases
- Smear and stains
- Microscopic examination
- Cultures
- Tissue biopsy
How are smears and stains prepared
- By rolling a small amount of specimen across a glass slide
What are the different types of smears and stains
- Gram stain
- Giemsa stain
- Wright stain
- Acid-fast Bacilli
- Tzanck smear
What does the gram and giesma stains tests for
Gram: bacteria
Giemsa: microbes in tissue, H.pylori, chlamydia, malaria, histoplasma
What does the wright stain, and Acid-fast bacilli tests for
W: differential staining of blood smears, bone marrow, and blood parasites
A: TB and other types of mycobacteria
What does Tzanck smear test for
HSV, bulbous diseases
What is a gram stain used for?
- Bacterial differential stain
*will differentiate between different types of bacteria based on cell walls
How will gram neg and gram pos stain
+ purple
- red (do not retain crystal violet but take up safranin counterstain)
*if there is bacteria from a sterile site that is significant
How does yeast stain?
Purple
*will be a long pseudohyphae
What organism can stain neg or pos
Gardnerella vaginalis
What bacteria’s do not stain
- Mycobacterium tuberculosis
*waxy coating (use acid fast) - Chlamydia trachomatis
How is bacteria classified
- Scientific name
- Stain
- Shape
- Need for O2
How will the stained bacteria be described
To their morphology
1. Coccus (spherical or oval)
2. Bacillus (rod-shaped)
3. Spiral or helical (twisted)
By arrangement
1. Chains
2. Clusters
What are common spherical bacteria (+ cocci)
- Staphylococcus species
*grapelike clusters - Streptococcus species
*spherical and arranged in chains or pairs
What are common spherical bacteria (- cocci)
- Neisseria species (pairs)
*N. Gonorrhea
*N. Meningitides - Moraxella catarrhalis
What are the three main species of staphylococcal
S. Aureus
S. Epidermidis
S. Saprphyticus
How are the staphylococcus species differentiated from each other
By coagulation test (and morphology)
When conducing the coagulation test how will the different staphylococcus species turn out
- S. Aureus in clumps
*enzyme is present - S. Epidermis and S. Saprophyticus does not clump
*enzyme is absent
How does streptococcus pneumonia stain?
Gram + (purple-ish) diplococci
*diplococci are oval with somewhat pointed ends
What are the gram negative coccobacilli
- Haemophilus species
- Bordetella
What are the gram + bacillus bacteria
- Clostridium botulinum
- Clostridium difficile
- Clostridium tetani (tetanus)
- Clostridium perfringes (gas gangrene)
- Listeria
- Corynebacterium
- Bacillus anthracis
What are the gram - bacillus bacteria
- Escherichia coli (E. coli)
- Pseudomonas aeruginosa
- Salmonella species
- Klebsiella pneumonia
What spirochetes are difficult to gram stain?
- Treponema pallidum
- Borrelia burgdorferi (Lyme disease)
- Leptospira (Leptospirosis)
*difficult to stain bc of shape
What are the gram negative spiral bacteria
- Campylobacter jejuni
- Helicobacter pylori
- Vibrio cholera
A patient presents with penile discharge and you suspect Neisseria gonorrhea, what findings on the gram stain would support your diagnosis?
Gram neg diplo cocci
A patient presents with burning, frequency, and urgency. Urine culture reveals a gram negative bacillus (rods). What is the most likely etiology?
E. Coli
Patient presents with fever and chills, culture results reveal gram positive cocci in clusters what is the most likely etiology?
Staphylococcus
Patient presents with fever, cough, and shortness of breath. CXR reveals and right lower lobe infiltrate and gram stain results demonstrate a Gram positive diplococci. What organism do you need to cover for when choosing your ATB?
Strep pneumonia
What type of bacteria does a Giemsa stain look for?
- Chlamydia
- Plasmodium (malaria)
- Other parasites
What is a wright stain use for?
- Used to differentiate blood cell types
*Erythrocytes stain pink to buff
*Platelets exhibit a light pale pink
*Leukocyte stain magenta purple
*Monocytes stains ground glass blue
*Lymphocytes stain clear sky blue
What is Acid-Fast Bacilli used for?
Suspect mycobacterium species infection
*mycobacterium tuberculosis
*monitor TB
When should you consider the AFB test?
- Immunocompromised systems
- travel
- Confinement (prison)
- Recent exposure tuberculosis
What is the AFB smear performed on?
Sputum
*takes about 24 hours
*AFB red rod shaped against light blue background
What is required with a AFB smear?
Culture required
*2-6 weeks
When is Tzanck smear used?
to diagnose herpes virus infections
*HSV
*Herpes zoster
*Varicella
What will be on the Tzanck Smear?
Multinucleated giant cells
*will be diagnostic for herpes virus
*epithelial cells infected with HSV
*culture is required to identify specific virus
What is a wet prep (saline wet prep) used for?
- Microscopic exam of vaginal discharge
- For suspect Trichomonas infections or bacterial vaginosis
- Can also indicate hyphae (yeast)
What are abnormal results of a wet prep?
- Flagellated protozoan vaginalis infection
- “Clue cells” grainy appearance
*epithelial cells surrounded by bacteria
*suggest BV - Stick like projections are hyphae (yeast)
What are affirm wet preps?
- Used for vaginal discharge are often combined with KOH test which allows you to test for
*BV
*trich
*yeast
*all from the same swab
What is aptima used for?
- A separate culture swab is needed for gonorrhea and chlamydia
What is a viral culture used for?
- Needed for herpes if it is visualized
When is a KOH prep used for?
Diagnosis of fungal infections
*tinea
*candidiasis
*will be a direct examination of skin, hair, nails, vaginal discharge, sputum
How do KOH prep work for fungal infections
- KOH destroys epithelial cells and debris other than fungus
- Identifies hyphae, mycelia and budding yeast cells
How do KOH prep work for vaginitis
KOH is added after saline wet prep
1. Will yield a positive whiff test (get a fishy odor)
*AKA amine odor test (suggest BV)
What is the Amstel criteria for BV
- Homogenous vaginal discharge
- pH >4.5
- Presence of clue cells in gram stain
- Positive whiff test
*need 3/4 for diagnostic
When is India ink prep used for?
Used to identify fungal organisms
*especially cryptococcus
*opportunistic yeast
How does an India ink prep work?
- The polysaccharide capsule present in yeast will exclude the paricles of India ink
*there will be a halo around the organism
When is Darkfield microscopy used?
To detect primary syphilis (treponema pallidum)
*a drop of exudate from chancre lesion is placed on the slide
*can also use rapid plasma reagin (RPR) to test for syphilis
When is scotch tape test used?
For diagnosis of pinworm infection enterobius vermicularis
How to conduct the scotch tape test?
- Nighttime collection while sleeping I
What are cultures used for
Laboratory controlled growth of microorganisms on special media to determine the cause of an infection
What is the incubation period time frame?
24-48 hours
How should and when should cultures be obtained?
- Obtained under sterile environments
- Before starting ATB
When are aerobic cultures used
For more superficial wounds since
*bc bacteria needs O2
When are anaerobic cultures used
For abscess or deep wound, tissue, or normally sterile body fluids
What do cultures confirm?
The identification of the organism
Why is susceptibility testing used (bacterial cultures)
To determine the organisms sensitive or Resistance to various ATB
*will show the MIC
What are the different types of viral cultures?
- Throat
- Nasopharyngeal
- Rectal
- CSF
- Vesicles
**slow growing takes at least 3-5 days
How fast do fungal cultures grow?
Slow growing
*1 week or months
*need a specialized culture media
When are blood cultures used?
When there is suspected septicemia or bacteremia
What is the collection protocol for blood cultures
Adult: 2
Peds: 1
*peripheral blood draw from 2 different sites
What will a negative blood culture show
- No growth for # of days
*consider the timing of collection visual ATB administration
What will a + blood culture show
Common blood pathogens reported
1. Staphlocccocus aureus
2. Streptococcus pneumonia
3. Haemophilus influenza
4. Enterococcus
5. Pseudomonas
What could be a contaminant of a + blood culture
- Staphylococcus epidermidis
When should cultures be performed/
Before ATB started
*if already started try to take sample before the second ATB dose
When is a urine culture done?
For a suspected UTI
*common pathogens e.coli, enterococcus, Proteus sp., Klebsiella
What is the collection technique for urine culture
- Midstream, clean catch sample
*can be contaminated by patient - Catheterized
*best sample to culture
*less risk of contamination
*urine is sterile
What is an insignificant and a significant result for a clean catch specimen
Insignificant: <10,000 CFU
Significant: >100,000 CFU (infection)
What is significant result for a catheter specimen catch
Any # of CFU is concern for infection
*if more than >3 organisms grow, it is a likely contaminant
When is a nasopharyngeal culture done?
When there is suspected active bacterial or viral infection or carrier state
How is nasopharyngeal collection done
- Swab deep in nasopharynx
- Don’t let swab touch skin
- Rotate swab and rest briefly
- Place swab in tube
What can lead to rapid viral identification of a nasopharyngeal swab
Immunofluorescence of nasal secretion
*PCR assay and antigen detection is more reliable
When is a throat culture used?
To differentiate viral from bacterial pharyngitis and identify carriers
What is the most common pathogen detected on a throat culture?
Group A beta hemolytic strep (GABHS)
*streptococcus pyogenes
*takes 24-48 hours to culture
What is the gold standard for diagnosis of acute pharyngitis due to GABHS
Throat culture
*if the rapid strep is + no need to perform culture
How can true streptococcal infection be confirmed?
By measurement of antistreptococcal antibody titers
*antistreptolysin O (ASO) titers (for complicating factors)
When is a sputum culture used
For suspicion of pneumonia or TB
Is salvia the same thing as a sputum collection
No
*the sputum most come from the lungs
What would be a poor sample of a sputum culture
> 25 squamous epithelial cells/hpf
What is cerebrospinal fluid culture indicated for
Suspected meningitis (bacterial or viral)
*collection from lumbar puncture for CSF (Sterile)
What are the + results (CSF)
Adults:
1. strep pneumonia
2. H. Influenza
3. neisseria meningitides
Peds
1. Enteroviruses (Coxsackie, Echovirus)
2. Group B Strep
3. E. coli
4. S.pneumonia
5. N. meningitis
What are the most common pathogens on a wound culture
Staphylococcus aureus
*MSSA (methicillin sensitive)
*MRSA (methicillin resistant)
When is a stool culture collected
When there is suspicion of infectious diarrhea
*most collect a series of fecal samples
What are the most common pathogens collected on a stool culture?
SSYCE
1. Salmonella
2. Shigella
3. Yersinia
4. Campylobacter
5. E.coli
*specifically request the bacteria (include ova and parasites)
When is a rectal culture done
When there is a suspected viral infection
When are Cervical and urethral cultures done?
- For genital lesions, abnormal discharge or itching
- Suspected STD, PID, urethritis (gonrrohea/chlamydia)
What is considered the gold standard for many disease processes
Tissue biopsy
*ultimate determination of etiology
