Clinical Microbiology Flashcards
Importance of clinical diagnostics (3)
Guide care of patients
Determine appropiate treatments for infections
Determine the risk of infectious organism transmission to other patients, the clinic, or public
Specimen collection can be
Blood, tissues, scraps, swabs, impression, translucidate, exudate, urine, misc fluids, feces, vomitus/sputum
Factors that determine what to collect
Clinical symptoms (type of infection and location)
Duration of infection
Diagnostic tests to be performed
What is the 1st step for accurate diagnostic testing
Proper specimen collection
Common specimen for bacterial infection in cats and dogs
From skin Ear swabs Urine Wound swabs and fluids Blood
Common specimen for bacterial infection in horses
Nasal swabs and fluids
Wound swabs and fluids
Common specimens for bacterial infection in food production animals
Post mordem tissue organ
What are the common specimens for detection of parasite infection
Feces Vomit Sputum Blood Muscle biopsy Skin scrap Urine, etc
Specimen collection depends upon additional factors such as
Host, parasite,stage or parasite in its life cycle, clinical symptoms
When is the best time to collect specimen
Before treatment
During acute state of disease for pathogen detection
How to collect specimens
Using aseptic techniques to avoid contamination of sample or clinic
Collect speciments that will be specific to the pathogen causing disease
Be patient and calm
Use collection techniques that limit the contamination flora from normal flora
Correct handling and transport depends on (3)
Pathogen type
Specimen type
Diagnostic test performed
Hadling and transport considerations (3)
Temperature
Moisture
Additive to preserve specimen and reduce contaminant growth
Phenotypic examinations
Microscopic examination
Culture /biochem tests for growth and to isolate pathogens
Immunochemical methods
Binding of specific antibodies and pathogens
Molecular diagnostics
Identification or markers in the genome or proteome
Concentration techniques
Increase concentration of pathogen material increases likelihood of pathogen ID
Very common for parasite diagnostic
Microscopic examination of phenotypic method
To see cell morphology
CANT SEE VIRUSES but can get info from them
Use staining to enhance visualization and analysis of tissues and cells
Staining techniques
Staining techniques
Simple or differential
Simple stain
1 dye
Identify morphology
Cellular arrangement
Differential stain
More than one dye
Can distinguish between different types of cells and structures in addition to morphology and cellular arrangement
Common tissue stain
Identify a wide range of normal and abnormal cells and tissues
Can identify bcteria, fungi, parasites and viral infection
Hematoxylin (basic stain)
Stains acidic or negatively charged components (nuclear components)
Chromatin and nuclei
COLOR PURPLE
Eosin (acidic stain)
Stains basic or positively charged components, i.e. Positively charged components and granules, EC components
)elastic fibers, muscle, RBC)
COLOR RED/PINK
Acis fats stain
To stainorganisms with impenetrable cell wall
Mycobacterium and cryptosporidium
Capsule stain
Negative staining technique
Endospore stain
Spores are dyed by heating malachite green dye
Flagella stain
Flagella re thickened with mordant to make thick enough to see by staining
Fungal stains
Gomori methenamine silver, periodic acid shiff
Parasite stains
They can also be seen without stains
Leishman stain and trichrome stain
T or F
Parasites can only be seen with leishman stain and trichrome stain
False
They can be seen without stains
Advantages of micro examination (4)
Determine cell/tissue morphology
Cellular association of bacteria, parasite, fungi
Morphology
Provides an impresson of the disease stage or severity
Immediate analysis
Disadvantages of micro examination
Mild/chronic infection may not be readily detection
Not all specimens can be used for diagnosis of some bacterial infections
Cultured methods of pathogens are only used for
Diagnosis of bacterial or fungal infection
Viruses and parasite grow poorly in cultures
T or F
Different bacteria will still grow in the same environment as others and have same nutritional requirements to survive
FALSE
Fastodious bacteria require
Specific nutrients and culture conditions
Nutrient media
Important for general growth
Slective media
Important for growth of your suspected pathogen type
Differential media
Most are selective media and helpfull in bacterial ID
Enrichment broth
Increase number of a specific bacterial type and inhibit growth of others
Biochemical testing
Helpfull in poathogen ID
Enzymes and fermentation
Basic nutrient media (3)
Trypticase soy agas (TSA) Luria bertani (LB) agar Mueller-hinton (MH) agar
Enriched nutrient agar media (4)
Blood agar
Brain heart infusion agar
Chocolate agar
Lysed-blood agar
Aerobic bacteria
Need O
Anaerobic bacteria
No O present in environment
Capnophites
Need CO2
Slective media for gram positive bacteria
Phenylethyl alcohol agar.
Slective media for fungi
Saboraud dextrose agar (SabDex) has low pH
Selective media for gram negative
Eosin methylene blue. Agar (EMB)
Columbia CNA agar contains
Colistin and Nalidixic acid for gram positive selection
Differential media
Helps determine bacterias identity
Blood agar
MacConkey agar (gram neg and lactose fermentation)
Mannitol salt agar (gram pos, mannitol fermentation)
CLED agar
What is CLED
Cysteine lactose electrolyte deficient
For unrinary bacteriology
Phenotypic methods of biochemical tests onm bacterial ID (3)
Enzyme production
Carbon source usage
Carbohydrate fementation
Enzyme production (4)
Catalase
Coagulase
Urease
Indole
Catalase
Breaks down hydrogen peroxidase
Coagulase
Causes fibrin in blood to clot
Urease
Hydrolyses urea
What is the carbon source usage
CIITRATE
Urine paddles
Provide semi-quantity colony count
Presumptive ID of many common uropathogens
Sides of urine paddle (2)
One is selective EMB media for gram negative
Other is non selective CLED media
At what temperature to you incubate an urine paddle and how long
37 celcius
18-24 hours
FlexCULT Vet UT gives what information about bacteria
Susceptibility information
What is an important tests for effective treatment of bacterial infections
Antibiotic sensitivity testing (AST)
Immunochemical tests detect
Pathogen specific antibodies or antigens
What is an antigen
Molecule that can trigger a host immune response
Antigens from pathogens can be (3)
The whole pathogen itself (only small part of surface is the antigen)
A molecule produced by pathogen
Pathogen molecules tat are presented on the surface of host cell
Immunochemical test exploits the principles of pathogen specific immune response to
Detect and ID pathogens
Common speciments for antibodies
IgG
IgM
IgG
Blood (common)
Tissue fluids
IgM
Blood
Indicators of active/recent infection (3)
Pathogen detection
Present or recent clinical symptoms of infection
Amount of titre of antibodies
T or F
Abscence of antibody detection may not mean abscence of pathogen
True
Specimen may have been taken before host pathogen specific antibody production
What does ELISA stands for
Enzyme linked immunosorbent assay
ELISA is
Specific antigen or antibody detection
ELISA characteristics
Detects immune response to virus, baceria, fngi or parasite
IS makes unique antibodies for each pathogen encountered
High sensitivity and specificity
Quantitative: amount of antigen or antibody present
T or F
ELISA is qualitative
False
Quantitative
What is an conjugate antibody
Antibody attached with indicator (e.g. Enzyme)
What is the Fc on the antibody
What is the variable region
FC is the constant region specific for each animal (top part)
Variable region is specific for antigen
What test can be a variation of lateral flow immunochromatic assay?
INDEXX SNAP test
INDEXX SNAP test detects
Antigen or antibody from species
Can the SNAP test be used for viruses?
Yes
Can be used for bacteria, virus and parasites
Immunofluorescence and immunochemistry can detect
Antigen in species
What does the agglutination test detect
Immune response to virus, parasites, bacteria or fungi
Advantages of immunochemistry tests (4)
ID pathogen when pathogen cannot be cultured
Most have high sensitivity
Most have high specificicty
Mid to high volume testing possible
Disadvantages of immunochemistry tests
Detection of antibody may not indicate an active infection
Antibody detection from specimen very early in infection may not be detected
What are identification of markers in the genome or proteome (3)
Techniques or test that determine pathogen ID by characteristic genetic or protein material
Uses pathogen specific genetic sequences to ID pathogen
Can use pathogen specific protein profile to ID pathogen
MALDI TOF identifies what and how
Bacteria
Mass spectrum
What does MALDI TOF detect
Protein pieces of pathogen by their mass and charge
Identification markers in genome
Uses pathogen specific genetic sequences to. ID pathogen
MULTIPLEX PCR or Microarrays
Real time PCR
MULTIPLEX detects
Nucleic acid from multiplw viruses, bacteria, fungi, parasite species in a single sample
Real time PCR is
Quantitive for pathogen
Advantages of molecular diagnostics (4)
Faster than cultured methods
Nucleic acid base techniques are highly sensitive
Accurate
High volume testing posible
Disadvantages of molecular diagnostics (3)
Expensive
Yes or no answer
Posible false negatives or positives
T or F
Viruses and parasites testing include MALDI TOF and culture based testig
FALSE
What is a false positive
Diagnostic test is positive for a pathogen or pathogen specific antibodies but patient is NOT infected with pathogen
What is a false negative
Test is negative for pathogen or pathogen specific antibody but patient is infected with that pathogen