Micro Basics, Lab Testing and Dx, and Antimicrobial Resistance Flashcards
What bacteria can transform into endospores?
- Bacillus anthracis
- Clostridium tetani
- Clostridioides difficile
- Clostridium perfringens
- Clostridium botulinum
Exam of fresh clinical specimens
wet mount
The following conditions may be dx’d with what method?
Actinomycosis
Chlamydia
cytomegalovirus
Genital herpes
giardiasis
Histoplasmosis
Leprosy
Lymphogranuloma venerium
Rubeola
Histology and Cytology
Examples of organisms that can be diagnosed with wet mount: sputum
Sputum for fungi
Examples of simple stains
Calcifour white, and india ink
Types of antigen detection test
-agglutination
- immunofluorescence
- enzyme linked immunosobent assay (ELISA)
When infection suspected in sterile body fluid, total protein, cell counts with differential, body fluid glucose, gram stain, culture.
Most compare with normal value for fluid.
Body fluid analysis
Presence of large number of white blood cells in any body fluid is an indication of..
Infection or inflammation
When is CSF assessed and what do they look for?
When meningitis suspected.
Color and clarity
Protein
Glucose
Wbc and differential
antibodies that cause clumping or glutination of type o red blood cells and cold temperatures test is used to detect antibodies that result from mycoplasma pneumoniae infection, viral pneumonia, or atypical pneumo
Cold agglutination
Shows current inflammatory process, sometimes used in the diagnosis of meningitis, pneumococcal pneumonia, sepsis, tuberculosis, and urinary tract infections
C reactive protein
Measure injury and damage to liver.
Liver function test
Measure gas exchange, shows resp failure due to pneumo, important for HAI pneumo and ventilator pneumo
Arterial blood test
General health assessment, white blood cells count and differential most useful for infection
Interpretation
Complete blood count
Increased WBC indicative of infection or inflammation
Reduced white blood cells counts
Leukopenia
WBC for Phagocytosis
Neutrophil
Increase in number if immature neutrophils
Left Shift
What is left shift indicative of?
Bacterial infection
What are increased lymphocytes indicative of?
Pertussis, syphilis, and toxoplasmosis
Lymphocytes with frothy cytoplasm (atypical or reactive lymphs) are indicative of
Viral infections like cytomegalovirus, or mononucleosis
Changes to this type of WBC is indicative of the following conditions:
EBV
TB
subacute bacterial endocarditis
syphilis
protozoan and rickettsial infections
Monocytes
Increase in eosinophils
Allergic reactions
parasitic infections
Dx test for the following conditions:
Rickettsial Diseases (RMSF, Q fever, epidemic typhus, rickettsial pox)
Weil-Felix agglutination
Indicators in Urinalysis
Color and clarity
Proteins
glucose
ketones
blood nitrate
leukocyte esterase
What do dipsticks test for?
Leukocyte esterase (WBC in urine) and nitrates (bacteria in urine)
Describe gram positive cell wall
Many layers of peptidoglycan forming a thick rigid structure
Describe gram negative cell wall
It’s an outer membrane composed of lipoproteins, lipopolysaccharides, and phospholipids.
What benefits do the gram negative cell wall provide?
the outer membrane evades phagocytosis
provides a barrier to certain antibiotics
confers properties of virulence (endotoxins)
What are the methods to identifying fungus?
Skin scraping and culture
Common examples of yeasts
- Candida spp.
- Cryptococcus neoformans
Common example of molds
- Aspergillus app
- Mucormycosis agents (rhizopus and mucor)
Example of dimorphic fungi
Pneumocystis jirovechii
How are most parasites diagnosed?
Microscopy* (direct exam of stool, urine, vag, or duodenal secretions
How is giardiasis dx?
Direct antigen detection
How are amebiasis, schistosomiasis, cysticercosis, echinicoccosis, and malaria diagnosed?
serology
Describe viruses
Obligate intracellular parasites (can only grow and reproduce in cells)
How to dx viruses
- Direct detection- microscope, ELISA, PCR
- Antibody assay
- Viral culture
This antimicrobial susceptibility test measures the zone of inhibition
Disk diffusion/ Kirby bauer
This antimicrobial susceptibility test measures the minimum inhibitory concentration of antibiotics
broth dilution or e-test
Basics for specimen collection and transport
- collect aseptically and place in sterile container
- some specimens may go directly into culture media for example blood specimens and nasal swabs
- prompt delivery to the lab
When should routine environmental testing occur?
- biologic monitoring of sterilization processes
- monthly cultures/endotoxin testing of water and dialysate in hemodialysis units
- short-term evaluation of ip measures or changes in IP protocols
What are two examples of when special environmental testing may be indicated?
- Fungal spores
- Legionella and water
Describe quality systems for lab
All policies procedures and processes are required to achieve quality and reliable testing
Closeness of the result of obtained to the true value and it’s measured by sensitivity and specificity
Accuracy
Lab personal expertise and Quality assessment (pre-analytical through post analytical)
Quality systems
Repeatability (same results on same sample when repeated)
Precision
External evaluation of the quality of laboratories performance
Proficiency testing program
Ability of a test to identify the presence of disease or illness correctly, absence of false negatives
Sensitivity
Equation for sensitivity
True positives / (true positives + false negatives)
The ability of a test to identify the absence of a disease or illness correctly, absence of false positives
Specificity
Equation for specificity
True negatives /( true negatives + false positives)
Microscopic of tissues, useful when agents difficult or impossible to culture
histology
study of cells
cytology
Study of bacteria, fungi, protozoa, viruses, and algae
Microbiology
What are the shapes of fungi?
Mycelial
Stalked
Budded
What bacteria have long chain fatty acids?
Fastidious, acid fast bacteria
How to stain fungi
Calcifour white, makes the fungi flourescent
When a DNA in the environment, possibly from dead bacteria, enters another bacterium
Transformation
Occurs when all or part of a plasmid is transferred from a donor to a recipient cell. The cell must be in direct contact and transfer occurs via the sex pills. Can occur between widely separated species, leaving to rapid dissemination of genetic information
Conjugation
Occurs when bacterial DNA is transferred from a donor cell to a recipient cell via virus capable of infecting bacteria
Transduction
Term meaning must reproduce within living cells, cannot live outside of another cell
Obligate intracellular parasite
Example of an obligate intracellular parasite
Virus
Type of microscope used to look at viruses
Electron scanning microscope
What is a virus called when it is outside of the host cell
Virion, metabolically inert and it does not grow or multiply until it enters a host cell
Three major methods to diagnose viral infections
- Direct detection in a clinical specimen
- Specific antibody assay to detect viral antibodies in the serum
- Viral culture
Aston based test that produces a reflection change for detection of influenza virus
OIA (optical immunoassay)
Late microscopy cell scrapings from infected sites that can detect cowdry type A inclusion bodies to detect what virus?
Herpes simplex virus
Test for HPV
paniculaoi (pap) smear
What are negri bodies used to diagnose?
Rabies
General test for viruses
- Microscopy
- EliSA
- PCR
- DNA probes
- Latex agglutination
- Virus culture
When should wet mount examination occur?
ASAP after collection
Describe nutrient agar
Support growth of wide variety of bacteria
Example of nutrient agar
tryptic soy agar with 5 percent sheep’s blood
Enrichment medium
Special nutrients necessary for growth of fastidious bacteria
Example of enrichment medium
chocolate agar for Neisseria meningitidis
Selective media
Contains chemicals or antibiotics designed to inhibit normal commensal bacteria
Example selective media
bismuth sulfate agar for the isolation of salmonella
Differential media
Stains colonies of specific organisms, while inhibiting the growth of others
Example differential media
acetate agar to differentiate between e coli and shigella
Chocolate agar used to id
Neisseria meningitidis
Bismuth sulfate agar used to isolate
Salmonella
Acetate agar used to..
Differentiate between e coli and shigella
Mackconkeys agar
Selective media
Examples of how to decrease HAI risk regarding environment
- cleaning high touch surfaces and routine environment
- Washing from clean to less clean areas
Example of how to decrease HAI risk regarding surgery
- Preoperative showering using antimicrobial soap
- treatment of remote site infections prior to surgery
Examples of how to decrease HAI risk regarding surveillance
- Active surveillance culturing for epi sig organisms based on facility’s epi
Examples of how to decrease HAI risk regarding personal hygiene
- maintaining good oral hygiene and caring for the mouth
- encouraging good genital/ perineal area cleansing
True or false: Never cohort patients with a common exposure to a disease
False - patients can be cohorted if exposed as long as individual private rooms are not available and patients are not immunocompromised
What cells release cytokines? What is the trigger?
T-Cells, part of cell mediated immune response triggered when dendritic cells displace antigens to T-Cells
What does the release of cytokines activate?
Macrophages that will kill the microbe
Methods to reduce microbial exposure for Immunocompromised patients regarding standard practices
isolation
HH
Methods to reduce microbial exposure for Immunocompromised patients regarding antibiotics
Prophylactic antibiotics
Methods to reduce microbial exposure for Immunocompromised patients regarding reservoirs
no plants/ flowers
no pets
IP for food and water
True or false: the presence of microbes in a clinical specimen indicates the presence of infection
False, could be colonized
Bacteria that can form endospores
Bacillus anthracis
Clostridium tetani
Clostridium difficile
Clostridium perfringens
Clostridium botulinum
Shapes of bacteria: round
Coccus
diplococcus
streptococcus
Staphylococcus
Shapes of bacteria - spiral
spirochete
vibrio
spiral
Shapes of bacteria- rods
Rod (Bacilli)
Diplobacillis
Streptobacillis
coco-baciliius
Process gram stain
crystal violet
iodine
decolorize alcohol
safranin (red)
single-celled human parasites
Protozoa
types of parasitic worms
flukes
tapeworms
roundworms
Types of ecotoparasites
Lice
Scabies
What is critical to a proper culture?
Choice of nutrients in Petri dish
Incubation time
temperature
What is the concern for improperly selected/ collected/ transported specimens?
-can generate misleading clinical data and lead to wrong treatment
How do labs assist in the id of an outbreak?
- confirm organism identity
- recognize unusual organism clusters
- detect unusual organisms
- detect unusual resistance patterns
Type of testing used to identify disease processes without signs or symptoms
Screening
Generally what are the sensitivity and specificity for screening tests?
High sensitivity, low specificity (require confirmation)
3 types of testing
Screening
Confirmation
Dx
Evaluation of someone suspected have a certain disease state/ characteristic
diagnostic testing
most common stain procedure to examine a specimen for bacteria or fungi
Gram stain
Exam of fresh clinical specimens under direct examination
Wet mount
Diagnostic testing that generally detects with the use of immunologic or serologic procedures
Antigen detection
What are the sources for antigen detection?
Serum
Body fluids
other clinical specimens
Diagnostic test that assesses host response- often referred to as serology
antibody detection
Most widely used dx test
PCR
Which type of bacteria have o-antigens?
Gram-negative
Which type of bacteria have Lipid A
Gram-negative
Which type of bacteria have teichoic acid?
Gram-positive
What is teichoic acid important for?
Antigenic - so helps with serological testing of gram + bacteria
What organism has cell walls with long chains of fatty acids?
acid-fast bacteria
Traits of acid-fast bacteria cell wall
contain mycolic acid= cord factor (VLCFA)
Impact of acid-fast bacteria on staining process
waxy surface that is impervious to chemicals or dyes
Important pathogens associated with mycobacteria
TB
Leprosy
Opportunistic Wound Infections
What cells can mycobacteria grow in?
macrophages
Acid fast stain process
stain with carbolfuschin
heat
decolorize with alcohol
counterstain methylene blue
special fluorescent stain that binds to chitin in cell walls of fungi
calcoflour white
what kind of microscope is necessary for calcoflour white stain?
flourescent microscope
What happens if a bacteria acquires an R plasmid?
renders that bacterium and it’s descendants immediately resistant to antibiotics if resistance genes are encoded on the plasmids
type of microscope for virus
Electron microscope
Part of virus outside of the host cell - metabolically inert (does not grow or multiply) until it enters a host cell
Virion
Light microscopy cell scrapings from infected sites can detect ____ inclusion bodies from herpes simplex virus
Cowdry type A inclusion bodies
What is the optical immunoassay used to test for?
influenza
when to examine a direct wet mount
ASAP after collection
Example of trophozite examined in stool under wet mount
Giardia lamblia
Example of organism examined on a wet mount in vaginal discharge or urine sediment
Trichomonas vaginalis
Example of an organism examined on a wet mount from liver abscess aspirate
Entamoeba histolytica
What does the choice of media depend on?
- Site being cultured
-growth requirements of common suspected pathogens
-liklihood of normal flora
Only aerobic growth- oxygen required
Obligate aerobe
Both aerobic and anaerobic growth, greater growth in presence of oxygen
Facultative anaerobe
Only anaerobic growth, ceases to grow in presence of oxygen
Obligate anaerobes
Only anaerobic growth, but continues in presence of oxygen- oxygen has no effect
aerotolerant anaerobes
Only aerobic growth, oxygen required in low concentration
microaerophiles
Gram negative diplococci
Neisseria meningitidis
Part of bacteria for sex
Pili
Part of bacteria to adhere to surfaces
fimbrae
Part of bacteria for motility
Flagella
When do bacteria form endospores?
when nutrients are depleted and environmental conditions are too harsh to grow and multiply
What antibiotics are mycobacteria resistant to?
beta-lactam antibiotics
bacteria that lacks cell wall and is resistant to antibiotics that attack the cell wall
mycoplasma
What do catalase test differentiate?
strep and staph
What is coagulase used to differentiate?
Staph aureus- positive from other staph like staph epidermidis
True or false: gram-positive organisms are generally tested for their ability to ferment the nutrient sugar named lactose
False- gram negative
True or false- Pseudomonas spp. and Proteus spp. are non-lactose fermenting gram-positive organisms
False- gram negative
CSF analysis- what to look for
viral and bacterial infections
tumors/ cancers of nervous system
bleeding/ hemorhaging from spinal cord
4 basic components of CSF
1) color and clarity
2) protein
3) glucose
4) WBC
How to tell a bacterial infection in CSF from viral or fungal
Cloudy
Increased WBC
Decrease Glucose
Increase neutrophils
increased neutrophils and cloudy
Precautions for immunocompromised patient suspected of having cryptococcal meningitis
Standard precautions
Who should get PEP if they had unprotected exposure to infected N. meningititidis patients in healthcare?
encotrachel intubation
airway suctioning
oxygen admin
Mode of transmission N. meningitidis
droplet to close contacts
- household members
- Childcare center personnel
- persons directly exposed to the patient’s oral secretions
Main selective pressure responsible for the increasing drug resistance seen in hospitals
antimicrobial resistance
Alter permeability of fungal membrane, inhibit membrane biosynthesis or DNA synthesis
antifungals
Inhibit formation of DNA precursors, DNA polymerase, and HIV reverse transcription.
Antivirals
Interfere with cell wall biosynthesis, inhibit bacterial ribosomes, interfere with DNA replication or RNA transcription, or inhibit metabolic pathways
antibacterial
bactericidal activity by inhibiting cell wall synthesis
Beta-lactam drug
Examples of beta lactam drugs
Penicillin
Cephalosporin
Monobactam
Carbapenem
Inhibit bacterial enzymes - important in DNA replication
Fluoroquinolones
example fluoroqunionlone
ciprofloxacin
Inhibit protein synthesis, mostly bacteriostatic therefore used for less serious infection
Macrolides
Example of macrolide
Azithromycin
Act at site of bacterial ribosomes and are used for combination therapy for serious or multi-drug resistant infection
aminoglycoside
Example of aminoglycoside
gentamicin
in this susceptibility testing, bacteria is spread in law fashion onto Mueller-Hinton agar, paper disks impregnated with a standard amount of antibiotic are placed onto the agar surface, the agar plate is incubated overnight, organism growth is either inhibited by the concentration of the antibiotic in the agar or not
Disk Diffusion - Kirby Bauer Method
Area in which the concentration of antibiotic prohibits the growth of the organism
Zone of inhibition
What is cold agglutination used to dx?
Atypical pneumonia- mycoplasma (no cell wall) and viral
Obligate intracellular parasites
Chlamydia
Rickettsia
Coxiella
Some Mycobacterium
Apicomplexans (plasmodium, toxoplasma gondii, crypto)
typanosomatids (Leismania and trypanosoma cruzi
some fungi- penumocystis jerovichi
CSF timeframe for transport
1 hour
Specimen collection and transport: site of collection
Collect from site where agent most likely to be found
Specimen collection and transport: time
Collect at optimum time (ie sputum early in the morning)
Collect before antibiotics
Specimen collection and transport: volume
Collect adequate volume
Specimen collection and transport: contamination
Collect aseptically to minimize or eliminate from contamination from indigenous floro
Specimen collection and transport: collection equipment
Use appropriate collection devices, transport media, and sterile, leak-proof containers
Specimen collection and transport: label
clearly label specimens including site of collection
ID specimen source/ site of collection
Specimen collection and transport: skin collection
If collected through intact skin, cleanse the skin with 70% alcohol and iodine solution first or CHG.
Specimen collection and transport: patient collecting their own specimen
provide clear instructions (ie clean catch urine or stool) to obtain best quality and allay fears
Specimen collection and transport: delivery to lab
Delivery pro,ptly to lab
Specimen collection and transport: protection for HCP
Wear proper gloves and PPE
Use safety devices
When to use cold agglutination
Mycoplasma pneumonia
Mononucleosis
Viral pneumonia
Difference in cerebrospinal fluid analysis between bacteria viruses and fungi
1) Bacteria are cloudy while viruses and fungi are clear or hazy
2) Bacteria have an increase in neutrophils while viruses and fungi have a decrease in neutrophils
3) Bacteria have a decrease in lymphocytes and monocytes while viruses and fungi have normal to increase lymphocytes and monocytes
What does c-reactive protein show
Liver inflammation
What is leukocytosis
White blood cell count is greater than 10,000
What is leukopenia and when do you see leukopenia
White blood cell count is less than 4,000 and see an overwhelming infection with aids, viral hepatitis, mononucleosis, and legionnaires disease
What type of agents increases the number of neutrophils?
Bacteria
What is weil Felix agglutination used for
Rickettsial agents
What is the high cold aglutinin test usually indicative of
Mycoplasma pneumonia, viral pneumonia, or atypical pneumonia
Absolute neutrophil count
Total number of neutrals in blood
When does the sedimentation rate increase?
With severe acute infection and inflammation
What test identifies exotoxins?
Eia
What test identifies gram-negative lipid a endotoxin?
Limitless amoebocyte lysate test
Examples of organisms that release exotoxins
Clostridium tetani
Corynebacterium diphtheriae
C diff
S aureus
Examples of organisms that release endotoxins
E coli
Salmonella
Shigella
Pseudomonas
Neisseria
H influenza
Bordetella pertussis
Vibrio cholera
What wbc count is indicative of pyuria j. Urinalysis?
> 10 WBC / mm^3
