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Urine cultures

15 min

Skills you'll build3 skills
  • Choose the correct sampling site for a catheter urine culture
  • Calculate CFU/mL from a colony count and the calibrated loop volume
  • Match a urine colony-count cutoff to the collection method and the organisms grown

Try first

Try first

A urine culture from a patient with an indwelling catheter arrives in a cup labeled "from drainage bag". What do you do?

Keep going to see the reasoning.

Right. Keep going to follow the reasoning.

Keep going to see the reasoning.

Keep going to see the reasoning.

Get the idea

Use the explanation to check your first decision.

Collecting a urine for culture

The distal urethra contains flora, so any urine that passes through it contains some contaminants. That is why urine culture is quantitative.1 The count means something only when the specimen is fresh. Organisms keep multiplying in urine left at room temperature, and the count becomes falsely high.

  • Culture unpreserved urine within about 30 minutes at room temperature. Otherwise refrigerate it at 2 to 8 °C for up to 24 hours or collect it into a boric acid preservative tube.2
  • For an indwelling catheter, disinfect the needleless sampling port and aspirate with a sterile syringe or cannula adapter. Never sample from the drainage bag.3
  • A suprapubic aspirate bypasses the urethra.1

Converting colonies to CFU/mL

A calibrated loop places a known volume of urine on blood agar and a second plate such as MacConkey. The plates are read at 16 to 24 hours, and negative plates are kept to 48 hours. CFU/mL = colonies counted ÷ inoculated volume (mL) for an undiluted urine specimen, so a 0.001-mL loop gives a factor of 1,000 and a 0.01-mL loop a factor of 100. Any further specimen dilution is multiplied in separately. The 0.001-mL loop is used for most specimens. The 0.01-mL loop is used for suprapubic aspirates and for suspected acute urethral syndrome in women.1

Interpreting the colony count

No single count separates infection from contamination. The laboratory's culture algorithm sets workup thresholds by collection method and patient group.1,2

Specimen and patientCount that can be significant
Voided urine, symptomatic woman10² to 10³ CFU/mL of one uropathogen
Voided urine, symptomatic man, or straight-catheter urine10³ CFU/mL or more
Suprapubic aspirateAny growth
Voided urine, no symptoms (asymptomatic bacteriuria)10⁵ CFU/mL or more of one organism

The 10⁵ CFU/mL criterion came from screening women without symptoms. It mainly defines asymptomatic bacteriuria.1 Three or more organism types at low counts usually indicate periurethral contamination. They are reported as mixed flora and not worked up.1

Follow the bench demonstration

Sources for this step
References
  1. Tille PM. Bailey & Scott's Diagnostic Microbiology. 15th ed. Elsevier; 2021.
  2. Miller JM, Binnicker MJ, Campbell S, et al. Guide to utilization of the microbiology laboratory for diagnosis of infectious diseases: 2024 update by the Infectious Diseases Society of America and the American Society for Microbiology. Clin Infect Dis. Published online March 5, 2024. doi:10.1093/cid/ciae104
  3. Centers for Disease Control and Prevention. Catheter-associated urinary tract infections (CAUTI): summary of recommendations. March 25, 2024. Accessed September 27, 2026. https://www.cdc.gov/infection-control/hcp/cauti/summary-of-recommendations.html

Watch one

Read each decision and its explanation.

A straight-catheter urine from a woman with fever and flank pain is plated with a 0.001-mL calibrated loop. At 24 hours the plate has 37 colonies of one lactose-fermenting gram-negative rod and nothing else.

What is the count, and does it require a workup?

  1. Read the loop volume on the worksheet: 0.001 mL.

    The loop volume sets the conversion factor.

  2. Find the factor: 1 ÷ 0.001 mL = 1,000 per mL.

    Each colony represents the organisms in 0.001 mL of urine.

  3. Count by colony type: 37 colonies of one type, with no other growth.

    Each organism type is counted separately.

  4. Multiply: 37 × 1,000 = 37,000 = 3.7 × 10⁴ CFU/mL.

    The colony count multiplied by the factor gives CFU per milliliter.

  5. Compare with the collection: a straight-catheter specimen is significant at 10³ CFU/mL or more.

    The threshold depends on how the urine was collected.

The count is 3.7 × 10⁴ CFU/mL of one organism, above the 10³ CFU/mL level for a straight-catheter specimen, so the isolate is identified and tested.

Practice this skill

Your turn

Problem 1 of 3 · Hints available

A urine plate inoculated with a 0.001-mL calibrated loop grows 48 colonies of one organism. What concentration does that represent?

The plate received only 0.001 mL. Convert the observed colonies to a full milliliter.

A 0.001-mL loop represents 1/1,000 of a milliliter, so multiply its colony count by 1,000. The factor of 100 applies to a 0.01-mL loop.

48 ÷ 0.001 = 48,000 CFU/mL. Interpret the count with the collection method and the patient population.

Hint
  1. Note what fraction of a milliliter the loop delivered.
  2. Divide the colony count by the loop volume in milliliters.

Review Quantitative culture and colony-count interpretation

Problem 2 of 3 · Hints available

A midstream urine from a woman grows three colony types, each at about 2 × 10³ CFU/mL. How is it reported?

Three organism types at low counts usually come from periurethral flora. Working them up reports contaminants as pathogens.

The three counts are about equal, and none is a predominant uropathogen. The pattern is contamination.

Growth of three or more organism types at low counts usually means periurethral contamination. It is reported as mixed flora and not worked up.

The 10⁵ CFU/mL criterion mainly defines asymptomatic bacteriuria. Growth was present, and the report describes it as mixed flora.

Hint
  1. Count how many organism types grew before looking at any single count.
  2. Consider the source of several organisms at low counts in a voided specimen.

Review Quantitative culture and colony-count interpretation

Problem 3 of 3 · On your own

A suprapubic aspirate from a 5-week-old infant is plated with a 0.01-mL calibrated loop. The plate grows 23 colonies of one organism. What is the count?

Show the answer

2,300 CFU/mL

A 0.01-mL loop gives a factor of 1 ÷ 0.01 mL = 100 per mL. 23 × 100 = 2,300 CFU/mL (2.3 × 10³ CFU/mL). Any growth from a suprapubic aspirate warrants a workup.

Review Quantitative culture and colony-count interpretation

Use it

Read the case evidence, then make each decision. The step is complete without it.

  • Harold Rackley, 78, has had an indwelling Foley catheter for 4 days and now has a fever.
  • Last night a urine labeled "from drainage bag" was plated before anyone read the label.
  • This morning it shows more than 10⁵ CFU/mL of three organism types.
  • A second specimen, aspirated from the disinfected sampling port, is plated with a 0.001-mL loop. It grows 64 colonies of one lactose-fermenting gram-negative rod.
Decision 1 of 2

What happens to the bag specimen's culture?

The organisms multiplied in the bag at room temperature. A high count from bag urine reflects that growth.

Collected a culture specimen from the drainage bag

Urine in a drainage bag has sat at room temperature, so organisms multiply and the colony count no longer reflects the bladder urine. A fresh specimen aspirated from the disinfected sampling port represents the current catheter urine.

Bag urine does not represent bladder urine. The port specimen gives the reportable count.

Any report from this culture would describe urine that stood in a bag. The comment states why no result is given.

Review Specimen collection

Decision 2 of 2

What count does the port specimen show?

This uses the factor of 100 for the 0.01-mL loop. A 0.001-mL loop gives a factor of 1,000.

Used the conversion factor for a different loop volume

A 0.001-mL loop carries 1/1,000 of a milliliter, so each colony represents 1,000 CFU/mL. Using the 0.01-mL factor of 100 reports a count 10 times too low and can drop a significant count below the laboratory's workup threshold.

This reports the colonies without converting for the volume plated. The loop delivered only 0.001 mL.

64 ÷ 0.001 mL = 64,000 CFU/mL (6.4 × 10⁴ CFU/mL) of one organism.

Review Quantitative culture and colony-count interpretation

The decision rests on the collection site named on the label. Urine from the drainage bag gives no reportable count. The fresh port specimen gave one organism at a count that represents his bladder urine.

For reference

Sources checked