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Urine Cultures (2)

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1
Q: What structures make up the urinary tract?
A: Kidneys, ureters, bladder, urethra
2
Q: What does UTI stand for?
A: Urinary tract infection
3
Q: What organs are involved in an Upper UTI?
A: Kidneys (pyelonephritis) and ureter (ureteritis)
4
Q: What organs are involved in a Lower UTI?
A: Bladder (cystitis), urethra (urethritis), prostate in males (prostatitis)
5
Q: Why are females more prone to UTIs?
A: The female urethra is shorter and in close proximity to the perirectal region, allowing organisms to easily reach the bladder
6
Q: How does sexual activity affect UTI risk in females?
A: Sexual activity can increase contamination of the female urethra
7
Q: Is urine normally sterile?
A: Yes, urine is typically sterile
8
Q: From where can urine become contaminated?
A: microbiota from Perineum, vagina, or urethra
9
Q: Why are quantitative cultures used in UTI diagnosis?
A: To discriminate between contamination, colonization, and infection
10
Q: What are the routes of infection listed for UTIs?
A: Ascending, hematogenous, lymphatic
11
Q: Which route of infection is most common?
A: Ascending
12
Q: What does “ascending” mean in community-acquired UTIs?
A: Bacteria moves up the urinary tract from urethra to bladder and potentially to kidney
13
Q: What healthcare-associated factors contribute to ascending infection?
A: Catheterization, cystoscopy
14
Q: How do organisms enter the bladder in healthcare-associated ascending infections?
A: They are pushed along the urethra into the bladder or migrate along the tract between the catheter and urethral mucosa
15
Q: What is the hematogenous route of infection?
A: Systemic infection can lead to seeding of kidneys
16
Q: Which organisms are examples of hematogenous spread to kidneys?
A: Staphylococcus aureus, Salmonella species
17
Q: What is the lymphatic route of infection?
A: Pressure on bladder causes lymphatic flow into kidneys
18
Q: Why is urine inhibitory to organisms? (4)
A: Low pH, high or low osmolality, high urea, high organic acid content
19
Q: How does constant flushing help prevent infection?
A: It eliminates bacteria
20
Q: What can lead to UTI by interfering with normal voiding?
A: Kidney stone or strictures
21
Q: What property does the bladder mucosal surface have?
A: Antibacterial properties
22
Q: What does the valve-like mechanism at the junction of the ureter and bladder prevent?
A: Reflux from bladder to upper UT
23
Q: What is uromodulin also known as?
A: Tamm-Horsfall protein
24
Q: What is the function of uromodulin (Tamm-Horsfall protein)?
A: Anti-adherence protein
25
Q: What do organisms adhere to in the urinary tract?
A: Vaginal and uroepithelial cells
26
Q: What happens during hydrolysis of urea?
A: Increase pH is toxic to kidney cells and stimulates formation of kidney stones
27
Q: What is the effect of increased pH on kidney cells?
A: It is toxic to kidney cells
28
Q: What does increased pH stimulate?
A: Formation of kidney stones
29
Q: What can uropathogens do to bladder epithelial cells?
A: Invade them and become intracellular bacteria that can shed as a result of exfoliation
30
Q: What are examples of other virulence factors?
A: Necrotizing factor, protease
31
Q: What are struvite crystals also known as? and what are they associated with?
A: Triple phosphates; High pH on urine microscopy.
32
Q: What urine specimens are unacceptable?
A:

Urine catheter tips (i.e. Foley catheters)

Pooled 24-hour urine

Unrefrigerated or unpreserved urine more than 2 hours old

More than 1 specimen/day

Non-sterile urines for anaerobic culture
33
Q: How long is refrigerated urine acceptable?
A: 24 hours
34
Q: What must be done if urine is unrefrigerated?
A: Specimen must be transported in preservation (0.5 mL boric acid)
35
Q: Why must manufacturer minimum volume be followed when using preservative?
A: To avoid inhibition of uropathogens
36
Q: What type of urine collection is discouraged for neonates, infants, and young children?
A: Pedibag urines, but can be analyzed if that’s the only way to obtain specimen
37
Q: How can a urine culture be ordered?
A: Stand-alone or as urinalysis (UA) with reflex to culture
38
Q: Under UCLA criteria, when can a UA reflex to culture be performed?
A: If no urine culture was collected in the past 24 hours and any one of the criteria is met on UA
39
Q: What UA findings meet criteria for reflex to urine culture?
A:

Leukocyte esterase is positive (positive, 1+, 2+, 3+) – evidence of host response

Nitrite is positive

WBC is >52/µL (9 WBC/HPF) – pyuria
40
Q: Is Gram stain typically performed for urine cultures?
A: No, typically not performed (available per request)
41
Q: What suggests contamination on Gram stain?
A: Squamous epithelial cells and many different bacterial morphotypes
42
Q: What media are used for urine cultures?
A: BAP and MAC
43
Q: Why may CNA agar be added to urine cultures?
A: To visualize gram positive microbiota (typically, gram negative will overgrow)
44
Q: What media combination is commonly used by hospitals for urine cultures?
A: CNA/MAC biplate
45
Q: Why are chromogenic media such as CHROMagar Orientation used?
A: To help distinguish uropathogens
46
Q: What is Columbia CNA agar used for?
A: Selective media for isolation of gram positive organisms
47
Q: Which agents in CNA agar inhibit gram negatives?
A: Colistin and nalidixic acid
48
Q: What can be observed about colonial morphology on CNA agar?
A: Media may exhibit multiple colonial morphologies from the same strain
49
Q: Which gram negatives may grow on CNA agar? examples?
A: Gram negatives that are resistant to colistin and nalidixic acid;
A: Proteus, Morganella
50
Q: What is another selective media for gram positives mentioned?
A: Phenylethylalcohol (PEA)
51
Q: How does Staph grow on PEA compared to CNA?
A: Better growth of Staph on PEA than CNA
52
Q: What does PEA inhibit?
A: Swarming Proteus
53
Q: What is done for sterile urine with no colony count?
A: Centrifuge urine, inoculate BAP and MAC with 1 drop of sediment and streak for isolation
54
Q: How are urological reconstructions with no colony count processed?
A: One drop of urine on each agar plate (BAP, CNA, MAC) and streak for isolation
55
Q: How is routine/non-sterile urine with colony count inoculated?
A: Inoculate media with 0.001 mL calibrated loop on BAP and MAC
56
Q: What does 1 colony equal in urine culture quantitation?
A: 1,000 CFU/mL
57
Q: At what temperature and conditions are urine cultures incubated?
A: 35–37°C at ambient air for minimum of 18 hours
58
Q: How long are sterile urines incubated?
A: 48 hours
59
Q: When can incubation be extended or plates incubated in CO₂?
A: Upon physician request
60
Q: Why might plates be incubated in the CO₂ incubator?
A: To enhance gram positive growth
61
Q: What pathogens are commonly recovered in urine cultures?
A:

Escherichia coli

Other Enterobacterales (i.e. Klebsiella species, Proteus species, Enterobacter species)

Pseudomonas aeruginosa (and other nonfermenters)

Staphylococcus aureus

Staphylococcus saprophyticus

Enterococcus species

Streptococcus agalactiae

Candida species (yeast)
62
Q: What are typical urogenital microbiota?
A:

Lactobacilli

Viridans Group Streptococcus

Coryneform bacteria

Coagulase negative Staphylococci
63
Q: According to the Clinical Microbiology Procedures Handbook, how is urogenital or skin microbiota handled in workup?
A: “Urogenital or skin microbiota that is at least 10 times less than the uropathogens is ignored for purposes of workup”
64
Q: When is antimicrobial susceptibility testing performed?
A: Once pathogens are identified on bacterial cultures
65
Q: What is antimicrobial susceptibility testing also called?
A: Susceptibility testing, sensitivity testing
66
Q: What is the purpose of antimicrobial susceptibility testing?
A: To determine whether the bacterial isolates can express resistance to antimicrobial agents selected for treatment
67
Q: Why is antimicrobial susceptibility testing a key component of the laboratory report?
A: It can help guide therapy for pathogens that have unpredictable susceptibility pattern
68
Q: What methods does the UCLA bacteriology lab use for susceptibility testing?
A: Broth microdilution, disk diffusion testing, and FDA cleared automated susceptibility testing (Vitek 2)
69
Q: When will procedures and methods for antimicrobial susceptibility testing be covered?
A: During AML training
70
Q: What will bacteriology section training focus on?
A: Understanding which agents to report for each organism and body site
71
Q: What is generally the criteria for a significant isolate?
A: ≥10⁵ (100,000) CFU/mL
72
Q: What is noted about protocol for significant isolates?
A: Protocol varies among different institutions
73
Q: What lower colony counts may be significant in certain cases?
A: 10⁴ or even 10²
74
Q: What is done for sterile urines?
A: ID and susceptibility testing on all isolates
75
Q: What is done for reconstruction urines?
A: ID and susceptibility testing on up to 2 organisms
76
Q: What is done if more than 2 organisms are isolated in reconstruction urines?
A: Report each organism using minimal/descriptive ID only
77
Q: What are examples of descriptive ID?
A:

Pseudomonas-like

Lactose positive/negative gram negative rod

Probable Staphylococcus aureus

Coryneform

Viridans strep-like

Coagulase negative Staphylococcus-like

Enterococcus-like
78
Q: What type of specimens are covered in this section?
A: Routine/Non-sterile urines
79
Q: When is ID and susceptibility testing performed for Staphylococcus aureus or gram negative rods?
A: If ≥50,000 CFU/mL of pure isolate
80
Q: When is ID and susceptibility testing performed for up to 2 organisms?
A: If ≥100,000 CFU/mL each
81
Q: What does “No Significant Growth” mean?
A:

<50,000 CFU/mL each of >2 organisms

<10,000 CFU/mL of non-pathogens
82
Q: When is “Contamination Suspected; Submit new specimen” reported?
A: ≥50,000 CFU/mL each of >2 organisms
83
Q: What is done for all other cultures that do not fit criteria?
A: Report quantitation with descriptive ID
84
Q: What is the example given for reporting quantitation with descriptive ID?
A: SA and EC 20,000 CFU/mL each – report 20,000 CFU/mL Probable Staphylococcus aureus and 20,000 CFU/mL Lactose positive gram negative rod
85
Q: What organisms are not routinely tested for susceptibility on urine cultures?
A:

Lactobacillus species

Staphylococcus saprophyticus

Aerococcus species

Beta Streptococcus

Corynebacterium, not urealyticum

Viridans group Streptococcus

Yeast
86
Q: Why is Staphylococcus saprophyticus not routinely tested for susceptibility?
A: Susceptible to commonly prescribed oral antibiotics for UTI
87
Q: What is noted about Beta Streptococcus susceptibility?
A: Routinely susceptible to Penicillin
88
Q: What type of hemolysis does E. coli show on BAP?
A: Beta or non-beta hemolytic colonies on BAP
89
Q: How is E. coli described on lactose media?
A: Flat lactose positive gram negative rod (some strains lactose negative)
90
Q: What is the most commonly isolated organism from urine cultures?
A: Escherichia coli
91
Q: What is the indole, MR, VP, LDC, and Motility reaction of E. coli?c
A: Positive (+) - INDOLE
A: Positive (+) - MR
A: Negative (−) - VP
A: Positive (+) - LDC
A: Positive (+) - MOTILITY
92
Q: How do Klebsiella colonies generally appear?
A: Generally raised, can be mucoid
93
Q: How is Klebsiella described on lactose media?
A: Raised lactose positive gram negative rod
94
Q: What are the key biochemical characteristics for the genus Klebsiella?
A:

VP +

ODC −

Motility −
95
Q: What test is used to differentiate between Klebsiella pneumoniae and Klebsiella oxytoca?
A: Indole
96
Q: What is the indole, VP, Motility, Gel, ADH, LDC, ODC reaction of Klebsiella pneumoniae?
Negative (-) - Indole
Positive (+) - VP
Negative (-) -Motility
Negative (-) - Gel
Negative (-) - ADH
Positive (+) - LDC
Negative (-) -ODC
97
Q: What is the indole, VP, Motility, Gel, ADH, LDC, ODC reaction of Klebsiella oxytoca?
Positive (+) - Indole
Positive (+) - VP
Negative (-) - Motility
Negative (-) - Gel
Negative (-) - ADH
Positive (+) - LDC
Negative (-) - ODC
98
Q: How can Enterobacter species appear on lactose media?
A: Can be lactose positive or lactose negative
99
Q: What are the key biochemical characteristics for the genus Enterobacter?
VP +

ODC + (differentiates from Klebsiella)

DNase −, Gel − (differentiates from Serratia)
100
Q: What is the LDC reaction of Enterobacter cloacae
A: Negative (−)
101
Q: What is the ADH reaction of Enterobacter aerogenes?
A: Negative (−)
102
Q: What is Enterobacter aerogenes currently reclassified as?
A: Klebsiella aerogenes
103
Q: What are the biochemical reactions of Enterobacter cloacae?
A:
Indole −
VP +
ADH +
ODC +
LDC −
Motility +
104
Q: What are the biochemical reactions of Enterobacter aerogenes?
A:
Indole −
VP +
ADH −
ODC +
LDC +
Motility +
105
Q: How is Serratia marcescens described on lactose media?
A: Lactose negative gram negative rod
106
Q: What type of pathogen is Serratia marcescens?
A: Significant nosocomial opportunist
107
Q: What pigmentation can some strains of Serratia marcescens exhibit?
A: Red/pink pigmentation
108
Q: How should red/pink pigmentation in Serratia be interpreted in relation to lactose?
A: Avoid interpreting this as lactose positive
109
Q: How can pigmentation be enhanced in Serratia cultures?
A: By holding cultures longer and leaving at room temperature
110
Q: Which other Serratia species are also pigmented?
A: Serratia rubidaea
111
Q: What are the key biochemical characteristics of the genus Serratia?
A:

VP +

Gel + / DNase +
112
Q: What test is used to differentiate Serratia marcescens from Serratia liquefaciens?
A: RAX (Raffinose, Arabinose, Xylose)
113
Q: What is the RAX reaction of Serratia marcescens?
A: RAX −
114
Q: What is the RAX reaction of Serratia liquefaciens?
A: RAX +
115
Q: What is characteristic of Serratia odorifera?
A: Pungent odor of potatoes/crushed vegetables
116
Q: What are the biochemical reactions of Serratia marcescens?
A:
Indole −
VP +
Gel +
DNase +
ADH −
ODC +
LDC +
Motility +
117
Q: On which media may Proteus swarm?
A: BAP/CHOC (rarely CNA)
118
Q: How is Proteus described on lactose media?
A: Lactose negative gram negative rod
119
Q: What is true of all members of the genus Proteus?
A: All members are TDA positive
120
Q: What smell may strains of Proteus mirabilis have?
A: “Chocolate” or devil’s food cake smell
121
Q: What are the ODC and indole reactions of Proteus mirabilis?
A: ODC +, indole −
122
Q: What are the ODC and indole reactions of Proteus vulgaris?
A: ODC −, indole +
123
Q: What are the ODC and indole reactions of Proteus penneri?
A: ODC −, indole −
124
Q: What are the biochemical reactions of Proteus mirabilis?
A:
Indole −
Urea +
H₂S +
TDA +
ODC +
Gelatin +
125
Q: What are the biochemical reactions of Proteus vulgaris?
A:
Indole +
Urea +
H₂S +
TDA +
ODC −
Gelatin +
126
Q: Is Pseudomonas aeruginosa a fermenter or nonfermenter?
A: Nonfermenter
127
Q: How is Pseudomonas aeruginosa described on lactose media?
A: Lactose negative gram negative rod
128
Q: What odors are associated with Pseudomonas aeruginosa colonies?
A: Grape/corn tortilla odor
129
Q: What sheen may Pseudomonas aeruginosa colonies exhibit?
A: Metallic sheen
130
Q: What pigment is associated with Pseudomonas aeruginosa?
A: Diffuse green pigment
131
Q: What is the oxidase reaction when Pseudomonas aeruginosa has a metallic sheen?
A: Oxidase (+)
132
Q: What are the biochemical reactions when Pseudomonas aeruginosa does not have a metallic sheen?
A: Oxidase (+) and acetamide (+)
133
Q: What type of hemolysis do Enterococcus colonies show?
A: Gamma colonies (can also be beta or alpha)
134
Q: What are the biochemical characteristics used to identify Enterococcus to the genus?
A:
Catalase (−)
PYR (+)
6.5% NaCl (+)
Bile-esculin (+) (non-Enterococcus group D are bile-esculin −)
135
Q: What is the treatment of choice for Enterococcus in urine cultures?
A: Ampicillin (concentrates well in the bladder)
136
Q: When is susceptibility testing performed for outpatient cultures?
A: Only upon request
137
Q: When is susceptibility testing automatically performed?
A: For inpatient cultures
138
Q: What method is used for full speciation (for Enterococcus) if needed?
A: API Strep
139
Q: How do Staphylococcus saprophyticus colonies appear?
A: Opaque, flat white colonies
140
Q: What are the biochemical reactions of Staphylococcus saprophyticus?
A:
Catalase (+)
Coagulase (−)
Novobiocin R (≤16 mm)
141
Q: Is routine susceptibility testing performed for Staphylococcus saprophyticus?
A: No, routine susceptibility not performed
142
Q: What antibiotics are commonly used to treat uncomplicated UTI caused by Staphylococcus saprophyticus?
A: Bactrim (SXT), fluoroquinolone, nitrofurantoin
143
Q: Staphylococcus saprophyticus is associated with which patient population?
A: Young, sexually active females and IUD
144
Q: What type of hemolysis does Streptococcus agalactiae show on BAP?
A: Narrow zone of beta-hemolysis on BAP
145
Q: What are the key biochemical characteristics of Streptococcus agalactiae?
A:
Catalase (−)
Lancefield group B (ID by latex agglutination)
146
Q: What are the other biochemical reactions of Streptococcus agalactiae?
A:
CAMP (+)
Hippurate (+)
6.5% NaCl (+)
Bile-esculin (−)
Bacitracin and SXT (R)
147
Q: In which patients should Streptococcus agalactiae be reported in any quantity?
A: Females of childbearing age (14–55 yo per protocol)
148
Q: Why is Streptococcus agalactiae significant in females of childbearing age?
A: Organism is implicated in neonatal infections
149
Q: Which organism can cross react with group B latex?
A: Streptococcus pseudoporcinus
150
Q: How can Streptococcus pseudoporcinus be identified?
A: MALDI-TOF
151
Q: What is the clinical implication of Streptococcus pseudoporcinus?
A: Premature rupture of membranes or spontaneous birth
152
Q: In which population is Streptococcus pseudoporcinus more prevalent?
A: African American
153
Q: How does Streptococcus pseudoporcinus differ from GBS (Group B streptococcus) on blood agar?
A: Larger zone of beta-hemolysis than GBS and LAP (+)
154
Q: How do most coryneform bacteria relate to the urogenital tract?
A: Most coryneform bacteria are urogenital microbiota, except for Corynebacterium urealyticum
155
Q: What type of infection does Corynebacterium urealyticum cause?
A: UTI with alkaline encrusted cystitis (stones)
156
Q: What urinalysis findings are associated with Corynebacterium urealyticum infection?
A:
Urinalysis pH 8–9
Struvite crystals present on UA microscopy
157
Q: What is the antibiotic resistance profile of Corynebacterium urealyticum?
A: Highly resistant to gram positive antibiotic, but susceptible to vancomycin (similar to Corynebacterium jeikeium)
158
Q: How does Corynebacterium urealyticum appear on Gram stain?
A: Small gram positive coccobacilli, PLGPR
159
Q: How do colonies of Corynebacterium urealyticum appear on BAP?
A: Slow-growing, non-hemolytic pinpoint colonies at 24 hour
160
Q: What is the growth requirement of Corynebacterium urealyticum regarding lipids?
A: Lipophile (will not grow if plated on CHOC)
161
Q: What are the biochemical reactions of Corynebacterium urealyticum?
A:
Catalase +
Urea: Rapid (+), <10 min (key characteristic)
Glucose (−)
Nitrate (−)
Esculin (−)
162
Q: How does Aerococcus relate to urogenital flora and Viridans group Streptococcus?
A: Aerococcus can be a member of the urogenital flora; differentiate from Viridans group Streptococcus if numbers are significant or pure
163
Q: How does Aerococcus urinae appear on Gram stain?
A: Gram positive cocci in clusters (Staph-like)
164
Q: What are the colony characteristics of Aerococcus urinae?
A: Small alpha hemolytic colonies (looks like Str. viridans)
165
Q: What are the biochemical reactions of Aerococcus urinae?
A:
Catalase (−)
6.5% NaCl (+)
166
Q: What are the Bacticard Strep reactions for Aerococcus urinae?
A: LAP +, PYR −, ESC v
167
Q: What is the availability status of Bacticard Strep?
A: No longer available
168
Q: How can full identification of Aerococcus urinae be performed?
A: Using API Strep kit
169
Q: What disease is caused by Salmonella typhi?
A: Typhoid Fever
170
Q: How common is Salmonella typhi in the USA and what is it often related to?
A: Rare in USA, often related to foreign travel
171
Q: What symptoms occur in the first 1–2 weeks of Salmonella typhi infection?
A: Fever, headache, and constipation
172
Q: What are the culture results in the first 1–2 weeks of illness?
A:
Blood cultures (+)
Stool and urine cultures (−)
173
Q: What symptom appears after 2 weeks of Salmonella typhi infection?
A: Diarrhea
174
Q: What are the culture results after 2 weeks of illness?
A:
Blood cultures (−)
Stool and urine cultures (+)
175
Q: What is the biochemical characteristic of Salmonella typhi on TSI?
A: Weak H₂S+ (mustache-look streak of TSI)
176
Q: What must be done if an organism is identified as Salmonella species?
A: Must serologically type
177
Q: What is the O antigen?
A: Heat stable somatic antigen
178
Q: What is the Vi antigen?
A: Heat labile capsular polysaccharide (mask O Ag)
179
Q: What must be done if the Vi antigen is detected?
A: Organism must be boiled and typing is repeated to detect the somatic antigen
180
Q: What does it mean if the somatic antigen is not detected after boiling?
A: Then it is not a Salmonella
181
Q: What is the purpose of abbreviated ID on urine cultures?
A: Commonly isolated organisms from urine cultures may be identified to species or genus using basic spot tests
182
Q: How is Escherichia coli identified when beta-hemolytic on BAP?
A: Spot Indole (+)
183
Q: How is Escherichia coli identified when non-hemolytic on BAP?
A: Spot Indole (+) & PYR (−)
184
Q: What colony morphology is associated with Proteus mirabilis?
A: Swarmer
185
Q: What test is performed for Proteus mirabilis?
A: Spot Indole (−)
186
Q: What colony morphology is associated with Enterococcus species?
A: Enterococcus-like
187
Q: What test is performed for Enterococcus species?
A: PYR (+)
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