URINE SAMPLES AND MOLECULAR TESTING Flashcards
Random samples
may be collected at any time, with no additional preparation or cleansing
random urine samples are used for
urine chemistry testing (creatinine, total protein,
electrolytes, microalbumin), but they are to be avoided for routine urinalysis or culture testing due
to the possibility of erroneous results and an increased chance of contamination
Midstream clean catch collection
comprises cleansing the skin near and around the urethra
Midstream clean catch is ideal for
urinalysis, bacterial culture,
and sensitivity testing
Catheterized specimens
collected by passing a hollow tube, or catheter, through the urethra
and into the bladder.
what are catheterized specimens useful for
bacterial culture testing, but it may
be used for other routine tests as well.
Suprapubic collection
a sterile environment when a needle is placed through the
abdomen and into the bladder.
Aspirated urine provides
a sterile sample that is free of outside
contamination and is ideal for bacterial cultures and cytologic examination
Nephrostomy tubes
catheters placed through the skin and directly into the kidney
What are nephrostomy catheters used for?
to drain or collect urine when output through the ureters in not possible. Samples may be
used for routine urinalysis testing or bacterial culture
The colony count is in colony forming units per mL
(number of colonies) × 100
No growth observed on media after 48 hours of incubation is
expected in normal clean-catch,
catheterized, suprapubic aspirate and in surgically obtained urine samples
Fewer than 10
colonies observed is
not considered a significant finding in clean-catch or catheterized specimens,
and no further workup is needed
**any bacterial growth of urine collected from sterile
sources is significant and requires further investigation
colony counts between 10
and 100 may be tested further if
a patient is having symptoms indicative of a urinary tract infection
(UTI)
> 100 colonies of mixed organisms exhibiting one
predominant organism is
a significant finding, and the predominant bacteria will be tested further
> 100 of a pure, single organism is
indicative of a UTI, and further workup is required to properly
identify the organism and perform antibiotic sensitivity testing for guide treatment options
Microscopic and macroscopic urinalysis findings are evaluated and correlated with
urine culture
findings in the determination of UTIs
which chemical reactions on a
urine dipstick indicate the presence or absence of bacteria in a sample?
Nitrite, pH, and leukocyte esterase
positive nitrite dipstick result indicates
infection is from common UTI-causing
bacteria, including E. coli, Klebsiella, Proteus, Pseudomonas, and Enterobacter species, as they will reduce
nitrate to nitrite
positive leukocyte esterase result indicates
UTI because WBCs are
commonly found in areas of infection
alkaline pH may indicate
the presence of infection-
causing bacteria in urine because some bacteria hydrolyze urea into the alkaline substance
ammonia
Macroscopic observations of WBCs and bacteria in urine sediment are
correlated
with urine culture results in the determination of a UTI
Colony morphology is evaluated by the following characteristics in urine cultures
- Colony size
- Form and margins
- Elevation
- Surface features, texture, and consistency
- Color, transparency, and iridescence
Colony morphology is categorized by
size, form, margins, and elevation characteristics
Colony size is categorized by diameter
o Pinpoint or punctiform < 1 mm
o Small 1–2 mm
o Medium 3–4 mm
o Large > 5 mm
Morphological Forms are categorized as
o Circular, symmetrical circle
o Irregular, lacking symmetry
o Filamentous, exhibiting threadlike branching
o Rhizoid, exhibiting a branching, rootlike shape
The margins, or edges, of a colony are most commonly evaluated as
o Entire, meaning smooth
o Undulate, meaning wavy
o Lobular, fingerlike growth spreading outward
o Scalloped, rounded projections resembling a scallop shell
o Filiform, thin and wavy layers spreading outward
Colony elevations are
categorized by the following shapes:
o Flat
o Raised
o Convex, curved or rounded upward
o Crateriform, sunken in the middle
o Umbonate, with the middle protruding upward
Textures are described with the following terms:
o Smooth,
o Wrinkled, shriveled
o Rough, granular
o Dull, no shine
o Glistening, shining
The consistency of colonies is described as the following:
o Moist
o Dry
o Viscid, thick and sticky
o Mucoid, moist and sticky
o Butyrous, butter-like
Colony transparency is categorized as
o Transparent, clear, see-through
o Translucent, semiclear, frosted-glass appearance
o Opaque, unable to see through
o Iridescent, color changing in reflective light
Sheep blood and chocolate agars often yield the following colony colors
o White
o Cream
o Yellow
Differential and selective medias can produce many colors based on the organism’s
biochemical properties such as:
o Pink
o Green
o Blue
o Black
Catalase positive
bubbling produced
catalase negative
no bubbling produced
coagulase positive
visible clumping
coagulase negative
no visible clumping or agglutination
oxidase test
is used for a presumptive identification of Neisseria species and P.
aeruginosa
oxidase positive
development of a dark-purple color within 10 seconds
oxidase negative
colorless, or remains the original color of the colony
Indole test
used for a presumptive identification of E. coli and differentiation of
swarming Proteus species
Indole positive
rapid development of a blue or green-blue color
Indole negative
no color change
PYR test
used to identify Enterococcus species and group A beta-hemolytic
streptococci through the presence of the enzyme pyrrolidonyl
PYR positive
development of bright red color
PYR negative
No color change or a yellow-orange color
Urease test
used to detect C. neoformans in sputum samples and differentiate
pathogenic Shigella and Salmonella species from nonpathogenic Proteus species in stool
cultures
Urease positive
color change to magenta
Urease negative
no color change, pH paper remains yellow
Triple sugar iron slant (TSI)
used for presumptive identification of many Gram-negative
bacilli, most commonly the enteric pathogens in the Enterobacteriaceae family.
TSI agar contains the following:
- Sugars — glucose, lactose, and sucrose
- Nutrient source — peptone
- Sulfur source — sodium thiosulfate
- Indicator — ferric ammonium citrate
- pH indicator — phenol red
TSI is inoculated using
a needle carrying a pure colony of the organism to be identified
K/K slant/butt
Slant, red; butt, red No sugars fermented, no reaction
K/A slant
Slant, red; butt, yellow Glucose fermented; lactose and sucrose not
fermented
A/A slant
Slant, yellow; butt, yellow Glucose fermented; lactose, sucrose, or
both fermented
G notation
Bubbles/splitting in the butt of the agar Gas production
H2S notation
Black precipitate H2S production
which testing method measures an organism’s ability to hydrolyze an
amino acid to form an amine?
Decarboxylase testing, also called Moeller’s method
Decarboxylase positive
purple color change compared to orange in the control tube
Decarboxylase negative
No color change, or yellow color in the test and control tubes
what test is performed to definitively identify yeast species in clinical
specimens
Carbohydrate utilization testing
Carbohydrate utilization positive
color change or growth around the disk
Carbohydrate utilization negative
no color change or growth around the disk
Motility testing is done to determine
if an organism is motile or not, allowing for further
differentiation among organisms
what are the two methods for determining motility
the hanging
drop method and the semisolid agar method
what objective is used to examine samples in the hanging drop method?
40x
what determines positive motility using the hanging drop method?
aka “true motility”
organisms change position
darting across field
what determines negative motility using the hanging drop method?
organisms may appear active
remain in same position
what determines positive motility using the semisolid agar method?
organisms spread out into medium from initial inoculation site
what determines negative motility using the semisolid agar method?
organisms will remain in same site as inoculation
what testing determines the identification and differentiation of Haemophilus species?
X and V factor
what organism is the most important to identify in X and V factor testing?
H. influenzae
what conditions occur from H. influenzae?
meningitis and pneumonia
what indicates a positive X and V factor test?
X & V: growth around the XV disk only
what indicates a positive V factor?
-growth around the V disk
-light growth around the XV disk
-no growth around X disk
what indicates a positive X factor?
-growth around the X disk
-light growth around the XV disk\
-no growth around the V disk
what indicates a negative XV factor?
growth on the entire surface of agar
what is latex agglutination testing used for?
qualitative and semiquantitative evaluations of virulent organisms
what organisms are used in latex agglutination testing?
Cryptococcus species
what is monoclonal antibody testing used for?
testing for antigens produced by H. pylori
or toxigenic C. diff strains
what components comprise organism identification and susceptibility testing?
-incubator
-automated reader
-data terminal
-printer
-LIS connectivity
what methods are used to determine biochemical reactions to known isolates?
-turbidity
-colorimetry
-fluorescent
-MALDI-TOF MS
what does MALDI-TOF MS stand for?
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry
what are the two phases of MALDI-TOF?
-ionization
-time-of-flight
what occurs during the ionization phase of the MALDI-TOF MS?
-sample is fixed to crystalline matrix
-then is bombarded by a laser
-laser vaporizes molecules into a vacuum and ionizes without destroying them
what occurs during the TOF MS phase of the MALDI-TOF MS?
-separates ions based on mass-to-charge ratio
-determines the time each molecule takes to reach detector
-patterns are compared to known patterns
what testing method allows for testing of multiple pathogens simultaneously?
multiplex molecular methods
what are multiplex systems used for the detection of?
respiratory or GI pathogens
what regions does genetic sequencing target?
16s ribosomal RNA in individual bacteria
what are the variable regions on the 16s gene?
V2, V3, V4, V6, V7, V8, V9
What is testing is used to find the correct agent and appropriate concentration to rid a bacterial infection?
antibiotic susceptibility and resistance testing
what are the most commonly used testing methods for antimicrobial susceptibility testing and resistance?
dilutions and disk diffusion
what method requires multiple tubes in varying concentrations of antibiotics with the test isolate?
broth dilution
what is considered the lowest concentration of drug necessary for inhibiting growth and multiplication?
MIC (minimum inhibitory concentration)
what is considered the lowest concentration of a drug resulting in death?
minimum bactericidal concentration
what method observes the zone size of bacterial growth inhibition?
disk diffusion
when is an organism considered susceptible?
when there is no bacterial growth around an antibiotic disk
when is an organism considered intermediate?
smaller zone, but not small enough to be considered resistant
may need a higher dose of antibiotics
when is an organism considered resistant?
having no zone of inhibition
