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Prof. Dr. Ali Avanoğlu
Vesicoureteral Reflux (VUR) • Diagnosis and evaluation

Urinalysis and Urine Culture in Children: How to Collect the Right Sample

Evaluation of vesicoureteral reflux (VUR) most often begins with a urine culture. A sample collected the wrong way can lead to unnecessary treatment or can mask a real infection. This page explains how to collect the right sample in infants and children, and what the results mean.

Who this is forFamilies asked to provide a urine sample from a feverish infant, who want to understand the result
Reading≈8 min
ByProf. Dr. Ali AvanoğluUpdated
This page is part of vesicoureteral reflux.Read the full treatment overview on the hub page
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01 · Why does this matter so much?02 · Types of samples: bag, midstream, catheter, suprapubic03 · Urinalysis: what does it check?04 · What does it mean if crystals are seen on urinalysis?05 · How is the culture result interpreted?06 · In practice: getting the right sample at home and in the clinic
In brief5 madde
  • Why does this matter so much?: Diagnosing a urinary tract infection (UTI) rests on two pillars: seeing inflammatory cells on urinalysis (pyuria), and a single organism growing in significant…
  • Types of samples: bag, midstream, catheter, suprapubic: In a diapered infant, the easiest method is an adhesive collection bag; however, bag urine is frequently contaminated with skin and bowel bacteria.
  • Urinalysis: what does it check?: Urinalysis is done with a dipstick test and under the microscope.
  • What does it mean if crystals are seen on urinalysis?: Crystals form when dissolved substances in the urine concentrate into particles visible under the microscope.
  • How is the culture result interpreted?: The amount of growth on culture is interpreted according to how the sample was collected.
01

Why does this matter so much?

Diagnosing a urinary tract infection (UTI) rests on two pillars: seeing inflammatory cells on urinalysis (pyuria), and a single organism growing in significant numbers on culture. If either is missing, or if the sample is contaminated, an ‘infection’ label is not reliable.

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  • This distinction is especially critical in vesicoureteral reflux. Reflux evaluation and treatment decisions are influenced by the number of febrile infections a child has had. A contaminated bag sample can steer this assessment in the wrong direction. Conversely, a culture taken after antibiotics have already started may not show a genuine infection.
  • In a feverish child, especially one with a reflux history, an appropriate urine sample is obtained before antibiotics whenever possible. However, in a child who appears ill, collecting the sample or waiting for the culture result should not delay treatment. In an infant under three months old, a fever of 38°C or higher requires urgent evaluation.
02

Types of samples: bag, midstream, catheter, suprapubic

In a diapered infant, the easiest method is an adhesive collection bag; however, bag urine is frequently contaminated with skin and bowel bacteria. For this reason, a bag sample can be used for screening on urinalysis. If the urinalysis is suspicious, a new sample by catheter or suprapubic method may be needed for culture. A bag culture alone does not establish a diagnosis of infection.

  • Bag: screening for urinalysis only; not suitable for culture
  • Midstream (clean catch): standard in a toilet-trained child
  • Catheter: standard for culture in a diapered, feverish infant
  • Suprapubic: low chance of contamination; can be used when catheterization is not feasible or results are equivocal
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  • In a child who has completed toilet training, a midstream sample is sufficient: the genital area is cleaned with water, the first part of the urine is passed into the toilet, and the middle portion is caught in a sterile container. In infants, stimulated voiding techniques (such as Quick-Wee) can be used to obtain a clean-catch sample, but they take time and are not always successful.
  • With a catheter sample, a thin, sterile catheter is briefly passed into the bladder. It is one of the methods commonly used for culture in a feverish infant; it can cause brief discomfort. With suprapubic aspiration, the sample is taken directly from the bladder through the lower abdominal wall with a thin needle. The chance of contamination is low, and it can be preferred when catheterization is not suitable.
03

Urinalysis: what does it check?

Urinalysis is done with a dipstick test and under the microscope. Leukocyte esterase, together with inflammatory cells seen under the microscope, supports the likelihood of infection. Nitrite positivity is also an important clue for certain bacteria. Because infants void frequently, nitrite can come back negative; a negative result alone does not rule out infection.

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  • A fresh sample matters. Get the urine to the lab quickly; if there will be a delay, follow the healthcare facility's storage instructions. Bacteria can multiply in a sample left at room temperature, which can make the culture misleading. Using a sterile container, keeping the lid closed, and labeling the sample also affect the result.
  • Growth alone without pyuria, especially in a child with no symptoms, is most often not infection but bacteria simply colonizing the urine (asymptomatic bacteriuria) or contamination; it does not require treatment. In a child with reflux, this distinction matters especially for avoiding unnecessary antibiotics.
04

What does it mean if crystals are seen on urinalysis?

Crystals form when dissolved substances in the urine concentrate into particles visible under the microscope. Seeing a small amount of crystals on a single urinalysis usually does not mean disease. The sample sitting for a while, concentrated urine, diet, and the urine's acidity can all affect the result.

  • Your doctor may reassess a one-time, small amount of crystals with a fresh sample if clinically needed.
  • An orange, brick-colored stain in a newborn's diaper can be related to urate crystals.
  • Recurrent or abundant crystals are interpreted together with symptoms and any history of stones.
  • See a doctor without delay if there is fever, vomiting, or marked lethargy, especially in a young infant who appears unwell.
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  • Reports may list names such as urate, calcium oxalate, or amorphous crystals. The type of crystal alone does not establish a diagnosis; some crystals can also form when a sample sits or cools. An orange, brick-colored stain in a newborn's diaper can be related to urate crystals in concentrated urine.
  • Repeated findings of abundant crystals on urinalysis are evaluated further. Flank or abdominal pain, blood in the urine, infection, or a family history of stones are important. Your doctor may repeat the test as needed and may order additional urine studies or an ultrasound.
05

How is the culture result interpreted?

The amount of growth on culture is interpreted according to how the sample was collected. The same threshold is not used for catheter, suprapubic, and midstream samples. The physician evaluates the type of organism, the inflammatory findings on urinalysis, the collection method, and the child's symptoms together.

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  • Growth of multiple organisms suggests the sample may be contaminated. Growth of a single organism together with pyuria is regarded as favoring infection. The time it takes for the culture and antibiogram to be ready can vary by laboratory. In a feverish infant who appears ill, an appropriate sample is obtained first whenever possible; treatment is not delayed for the culture result.
  • In a child on antibiotic prophylaxis, the type of organism and its resistance pattern affect treatment. If a febrile infection develops, share the culture result with the healthcare team following the child.
06

In practice: getting the right sample at home and in the clinic

If a bag is used, the skin is cleaned with soapy water and dried, the bag is applied, and the infant is checked frequently; if no urine has come after 20–30 minutes, the bag is replaced. As soon as urine appears, the bag is removed right away, transferred into a container, and taken to the lab. If the infant has a fever and the urinalysis is suspicious, don't hesitate to go to a healthcare facility for a catheter sample; it's a matter of seconds.

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  • For a midstream sample, cleaning front-to-back and keeping the legs apart in girls, and gently retracting the foreskin without forcing it in uncircumcised boys, reduces contamination. The sample does not have to be the first morning urine; what matters is collecting it correctly and getting it to the lab quickly.
  • For a child with known or suspected reflux, contact the healthcare team for any unexplained fever. Getting an appropriate urine sample before antibiotics makes diagnosis easier; treatment is not delayed in a child who appears ill. In an infant under three months old, a fever of 38°C or higher requires urgent evaluation.
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Frequently asked questions
Bacteria grew in a bag urine sample — should antibiotics be started?
No; a bag culture alone is not enough to decide on starting antibiotics. Contamination is common in bag samples. In a feverish infant or one with a suspicious urinalysis, the doctor may repeat the culture with a catheter or suprapubic sample. This process should not delay treatment in an infant who appears ill.
Does catheterizing an infant for urine cause harm?
Generally, no permanent harm. A thin, sterile catheter is briefly passed into the bladder and removed right away. The infant may be briefly uncomfortable; there is a small, though nonzero, risk of infection or irritation from the procedure. It's one of the methods commonly used to get a reliable culture sample in a feverish infant.
Can antibiotics be started without waiting for the culture result?
Yes. In a feverish infant who appears ill, an appropriate urine sample is obtained first whenever possible; but collecting the sample or waiting for the culture result should not delay treatment. Once the culture result is back, the physician decides whether to continue, change, or stop the medication. In an infant under three months old, a fever of 38°C or higher requires urgent evaluation.
The urinalysis is clean but my child's fever continues — what should I do?
A properly collected, clean urinalysis significantly lowers the likelihood of a UTI, and another source for the fever is looked for. But if the fever continues without explanation, especially in a child with reflux, the urinalysis and culture can be repeated after 24–48 hours. If there is worsening, vomiting, or lethargy, seek care without waiting.
Does seeing crystals on urinalysis mean kidney stones?
No. Seeing crystals on a single urinalysis does not by itself establish a diagnosis of kidney stones. If crystals recur, or if there is pain, blood in the urine, infection, or a family history of stones, your doctor may order additional urine studies and an ultrasound.
←Previous • Diagnosis and evaluationDMSA Renal Scan: Scarring and Function
Related pagesFull index →
Kidney health and infectionPyelonephritis in Children (Febrile UTI): Symptoms and When It's an EmergencyPyelonephritis is a febrile urinary tract infection (febrile UTI) in which bacteria travel up from the bladder and reach the kidney tissue. In children, it is the most common way kidney reflux first comes to light, and it is the main cause of scarring — which is why rapid diagnosis and timely treatment matter so much. This page covers symptoms by age, the warning signs for urgent care, how treatment is planned, and what is investigated afterward.Diagnosis and evaluationVUR Evaluation After a Febrile Urinary Tract Infection: Who Needs a VCUG?Roughly 25–40% of children who have a febrile urinary tract infection (UTI) are found to have vesicoureteral reflux (VUR). But that doesn't mean every child needs an immediate VCUG. This page explains which test is done for whom, in what order, and when, after an infection.Kidney health and infectionRecurrent Urinary Tract Infection in Children and VURRecurrent urinary tract infection in a child is a warning sign that calls for investigating an underlying cause; the most common causes are kidney reflux (vesicoureteral reflux, VUR), constipation, and voiding dysfunction. This page covers the definition of recurrent infection, its causes, which tests are done and when, and prevention measures that can be applied at home.After treatment and follow-upIf a Febrile Urinary Tract Infection Occurs After TreatmentHaving a febrile urinary tract infection (UTI) after vesicoureteral reflux treatment (endoscopic injection or ureteral reimplantation) understandably worries families. It does not always mean the treatment has failed; however, the cause needs to be investigated in a systematic order. This page explains the path followed, from culture through to DMSA.
Vesicoureteral Reflux (VUR) topic clustersMain treatment page →
Basics 6Diagnosis and evaluation 6By age and special situations 5Bladder and bowel 5Treatment pathways 10Kidney health and infection 5After treatment and follow-up 6
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