Urine culture results: what CFU/mL counts, mixed flora and sensitivities mean
Urine culture (Urine C&S) · Urine culture and sensitivity (C&S) · reported in Colony-forming units per milliliter (CFU/mL), often written as 10^3, 10^4 or 10^5 (1,000, 10,000 or 100,000); organism name; sensitivities reported as S, I or R with or without a minimum inhibitory concentration (MIC) in µg/mL
A urine culture is the laboratory test that grows the bacteria in a urine sample on nutrient plates, counts them in colony-forming units per milliliter (CFU/mL), identifies the species and tests which antibiotics stop it (the sensitivity or susceptibility part of a culture and sensitivity, C&S). It is the definitive test for a urinary tract infection. A normal result is no growth, or fewer than 10,000 CFU/mL of skin and genital bacteria; the classic threshold for infection is 100,000 CFU/mL (10^5) or more of a single organism, although lower counts are treated as significant in people with symptoms.
Most results fall into one of four patterns. No growth or insignificant growth means no bacterial infection was found (though symptoms may still have another cause). A single organism at 100,000 CFU/mL or more, usually Escherichia coli, is a positive culture and comes with a sensitivity table marked S (sensitive), I (intermediate) or R (resistant) for each antibiotic. Counts between 10,000 and 100,000 of one organism are a gray zone read alongside your symptoms and the dipstick. And mixed flora, meaning two or more species each at low counts, almost always means the sample was contaminated during collection and should be repeated rather than treated.
A culture usually takes 24 to 48 hours for a preliminary result and 48 to 72 hours for the final identification and sensitivities. Because that is longer than most people with a bladder infection are prepared to wait, uncomplicated cystitis in healthy women is often treated on symptoms and dipstick alone; the culture is reserved for infections that are recurrent, complicated, in men, in children, in pregnancy, after failed treatment or in anyone with fever and flank pain, where knowing the organism and its resistances changes management.
Urine C&S at a glance
- What it is: urine grown on culture plates for 24 to 72 hours to count (CFU/mL), identify and antibiotic-test any bacteria.
- Normal: no growth, or under 10,000 CFU/mL of mixed skin or genital flora. Positive: 100,000 CFU/mL (10^5) or more of one organism.
- Lower counts matter with symptoms: 1,000 CFU/mL or more (even 100 CFU/mL of E. coli) in a woman with cystitis symptoms, 1,000 in men, 100 to 1,000 in a catheter sample, any growth from a suprapubic aspirate.
- Mixed flora (two or more species, low counts) means contamination; repeat with a clean-catch or catheter sample rather than treating.
- The sensitivity report lists each antibiotic as S (sensitive), I (intermediate) or R (resistant) and guides the choice of treatment.
- Timing: preliminary result in 24 to 48 hours, final with sensitivities in 48 to 72 hours; a negative result is usually reported after 24 to 48 hours.
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What Urine C&S measures
In the laboratory a calibrated loop transfers a fixed volume of urine, usually 1 microliter (0.001 mL), onto agar plates that are incubated at 35 to 37°C for 18 to 24 hours and sometimes 48. Each living bacterium grows into a visible colony, so counting colonies and multiplying by 1,000 gives CFU/mL. Colonies are identified by their appearance, biochemical reactions or mass spectrometry, and a pure growth of a likely pathogen is then tested against a panel of antibiotics, either by measuring the zone of no growth around antibiotic discs or by finding the minimum inhibitory concentration (MIC). Results are reported as S, I or R against standardized breakpoints.
The 100,000 CFU/mL threshold dates from the 1950s, when Edward Kass showed that counts this high in clean-catch samples from women without symptoms reliably separated true bladder bacteriuria from contamination. Later work showed it misses about half of genuine infections in women with symptoms, whose bladder counts are often 100 to 10,000 CFU/mL; a 2013 study comparing midstream samples with catheter samples found that even 100 CFU/mL of E. coli in a symptomatic woman's midstream urine predicted true bladder infection 93 percent of the time, whereas enterococci and group B streptococci in the midstream sample usually came from the vagina and skin. Thresholds therefore depend on symptoms, sex and how the sample was collected.
Collection drives the result. A clean-catch midstream sample from a woman is contaminated about 30 percent of the time, and trials show cleansing wipes change this little. Samples should reach the lab within 2 hours or be refrigerated (or collected in a boric-acid preservative tube), because bacteria double every 20 to 30 minutes at room temperature and a delay turns an insignificant count into a falsely significant one. Catheter samples largely avoid contamination; bag samples in infants are contaminated so often that a positive result must be confirmed by catheter or suprapubic aspiration before treatment. Antibiotics taken in the preceding days can suppress growth and produce a falsely negative culture.
Normal range for Urine C&S
Reference ranges vary between labs and by age, sex and pregnancy. Use the range printed on your own report.
| Group | Typical range (Colony-forming units per milliliter (CFU/mL), often written as 10^3, 10^4 or 10^5 (1,000, 10,000 or 100,000); organism name; sensitivities reported as S, I or R with or without a minimum inhibitory concentration (MIC) in µg/mL) | Notes |
|---|---|---|
| No growth | No bacteria grew after 24–48 hours | The normal result. Persisting symptoms with no growth point to urethritis (chlamydia, gonorrhea), vaginitis, interstitial cystitis, prior antibiotics or an organism that needs special culture. |
| Insignificant growth | Below 10,000 CFU/mL (less than 10^4), usually of skin or genital organisms | Reported as 'no significant growth' or 'normal urogenital flora' by many labs. Counts this low in a symptomatic woman can still be a true infection if the organism is E. coli and white cells are present. |
| Mixed flora | Two or more species, typically each below 10,000–100,000 CFU/mL | Contamination during collection in the great majority of cases; no sensitivities are run. Repeat as a careful midstream or catheter sample if symptoms persist. Genuinely polymicrobial infection occurs mainly with catheters, stones or fistulas. |
| Equivocal | 10,000–100,000 CFU/mL (10^4 to 10^5) of a single organism | Significant with symptoms and pyuria, particularly in men (where 1,000 or more is used), in catheter samples and with a typical uropathogen; often repeated if there are no symptoms. |
| Positive (significant bacteriuria) | 100,000 CFU/mL (10^5) or more of a single organism | Classic Kass criterion; reported with identification and sensitivities. Asymptomatic bacteriuria if there are no symptoms (not treated outside pregnancy or pre-procedure); infection if there are. |
| Lower thresholds that count with symptoms | Women with cystitis symptoms: 1,000 CFU/mL or more (100 CFU/mL of E. coli); men: 1,000 or more; catheter specimen: 100–1,000 or more; suprapubic aspirate: any growth | Infectious Diseases Society of America and European guideline definitions. Labs differ in the lowest count they report; many do not quantify below 1,000 or 10,000. |
| Pregnancy | 100,000 CFU/mL or more on screening culture is treated; group B streptococcus at any count is recorded | Group B strep in urine during pregnancy means heavy colonization and triggers antibiotics during labor to protect the baby, whatever the count. |
| Yeast (Candida) | Reported in CFU/mL when grown | Usually colonization of a catheter or in diabetes; treated only with symptoms, a transplant, neutropenia or before a urological procedure. |
Positive urine culture
A positive culture means a single organism grew at a count that exceeds the threshold for your situation, most often 100,000 CFU/mL or more. In 75 to 95 percent of uncomplicated infections the organism is Escherichia coli from the bowel; Klebsiella pneumoniae, Proteus mirabilis, Enterococcus faecalis and, in sexually active young women, Staphylococcus saprophyticus make up most of the rest. Pseudomonas, Enterobacter, Serratia and resistant organisms are more typical of hospital-acquired infection, catheters, recent antibiotics and structural problems. The report then lists which antibiotics the organism is sensitive to, so treatment can be chosen or adjusted; S means standard doses should work, R means they will not, and I means they may work at higher doses or where the drug concentrates in urine.
Whether a positive culture needs antibiotics depends entirely on symptoms. With burning, urgency, frequency, pelvic pain, fever or flank pain it is an infection and is treated according to the sensitivities. Without any urinary symptoms it is asymptomatic bacteriuria, which is common in older women, people with diabetes and anyone with a catheter, and which is not treated except in pregnancy and before urological procedures that breach the lining of the urinary tract, because antibiotics in other groups do not prevent infections and do cause harm. Cloudy or strong-smelling urine without symptoms does not change this.
Resistance matters. In many parts of the United States 20 to 30 percent of E. coli from community infections are resistant to trimethoprim-sulfamethoxazole and 10 to 20 percent to fluoroquinolones, while resistance to nitrofurantoin and fosfomycin remains under 5 percent; extended-spectrum beta-lactamase (ESBL) producers resist most oral options and may need intravenous treatment. If you were started on an antibiotic before the culture came back and the organism is reported R to it, your clinician will switch; if you are already improving, some clinicians will finish the course anyway because urine concentrations of many antibiotics exceed laboratory breakpoints.
Common causes
Acute cystitis
Bladder infection, the most common reason for a positive culture; E. coli in 75 to 95 percent of cases in healthy women. Culture is optional in a first uncomplicated episode but useful when symptoms recur within weeks.
Pyelonephritis
Kidney infection with fever, flank pain and often vomiting; a culture (and sometimes blood cultures) is always sent because treatment is longer and resistance changes the choice of drug.
Asymptomatic bacteriuria
A significant count with no symptoms, found in 1 to 5 percent of young women, up to 20 percent of women over 80, 25 to 50 percent of nursing-home residents and virtually all people with long-term catheters. Not treated except in pregnancy and pre-procedure.
Contamination and delayed processing
Genital or skin flora in the cup, or bacteria multiplying during a delay before plating, can push counts above 10,000 or even 100,000 CFU/mL. Mixed species, no white blood cells and squamous epithelial cells on the urinalysis point to this.
Catheter-associated bacteriuria
A catheter is colonized at 3 to 7 percent per day, so nearly everyone catheterized for a month has a positive culture. Infection is diagnosed by fever or new symptoms with 1,000 CFU/mL or more, not by the culture alone; the catheter is changed before the sample is taken.
Prostatitis and male urinary infection
In men a count of 1,000 CFU/mL or more is significant. Bacterial prostatitis, an enlarged prostate with incomplete emptying and strictures are the usual underlying reasons, and infection in a man is treated for longer.
Kidney stones and structural abnormalities
Proteus and other urea-splitting organisms grow in and around struvite stones; reflux, obstruction, diverticula and fistulas keep bacteria in place. The same organism returning after treatment is a clue to a structural cause.
Pregnancy
Slower urine flow makes bacteriuria more common (2 to 10 percent) and more likely to ascend; a positive screening culture is treated regardless of symptoms, and group B streptococcus in urine at any count leads to antibiotics during labor.
Recurrent infection and resistant organisms
Recent antibiotics, hospital stays, travel and care-home residence select for resistant E. coli and Klebsiella (ESBL, fluoroquinolone resistance); cultures in these settings are essential because empiric choices often fail.
Symptoms that can go with it
- None, in asymptomatic bacteriuria and contamination
- Burning or stinging on urination, needing to go often and urgently, passing small amounts
- Pressure or cramping low in the abdomen, cloudy or blood-tinged urine
- Fever, chills, flank or back pain, nausea and vomiting with kidney infection
- Perineal, lower back or rectal pain, difficulty urinating and fever in men with prostatitis
- New incontinence, retention or a change in catheter drainage in people with catheters, alongside fever
- In infants and young children, unexplained fever, poor feeding, irritability or vomiting
Negative urine culture (no growth) with symptoms
A culture that grows nothing, or only insignificant mixed flora, rules out a typical bacterial urinary infection in most cases, and if your symptoms have gone that is the end of it. When symptoms persist despite a negative culture, the question becomes what else causes burning, frequency or pelvic pain. The most common answers are urethritis from chlamydia, gonorrhea, mycoplasma or herpes, which need specific swab or urine nucleic acid tests rather than culture; vaginitis (yeast, bacterial vaginosis, atrophic vaginitis after menopause), which causes external burning; and antibiotics taken in the days before the sample, which suppress growth without necessarily having cleared the infection.
A negative culture with white blood cells still present on the urinalysis, called sterile pyuria, has a longer list: a partially treated infection, kidney stones, interstitial cystitis (bladder pain syndrome), urinary tuberculosis, fungal infection, inflammation of adjacent organs such as appendicitis or diverticulitis, kidney inflammation from medications, and, over 50, bladder cancer. Some laboratories do not report counts below 1,000 or 10,000 CFU/mL, so a genuine low-count infection in a symptomatic woman can be reported as negative; if symptoms are typical and a dipstick shows white cells and blood, many clinicians treat as cystitis despite the culture.
Common causes
Urethritis from a sexually transmitted infection
Chlamydia, gonorrhea, Mycoplasma genitalium and trichomonas cause burning and discharge but do not grow on standard urine culture; a first-void urine nucleic acid test or swab is needed.
Vaginitis or atrophic changes
Yeast infection, bacterial vaginosis and estrogen deficiency after menopause cause burning as urine passes over inflamed tissue; itching, discharge and external soreness point this way.
Recent antibiotics
Even a single dose can stop bacteria growing on the plate while symptoms continue; tell the lab and your clinician about any antibiotics in the previous week.
Interstitial cystitis (bladder pain syndrome)
Chronic bladder pain, urgency and frequency with repeatedly negative cultures, typically in women, worse with bladder filling and certain foods; diagnosed after infection and other causes are excluded.
Low-count infection below the lab's reporting threshold
Bladder counts of 100 to 1,000 CFU/mL cause real symptoms in women but may be reported as no significant growth; pyuria and a typical history are treated by many clinicians regardless.
Organisms that need special culture
Mycobacterium tuberculosis, Ureaplasma, anaerobes and some fastidious bacteria do not grow on routine plates; sterile pyuria with risk factors prompts specific testing.
Stones, tumors and neighboring inflammation
Kidney or bladder stones, bladder cancer, appendicitis and diverticulitis can irritate the urinary tract and produce white cells and blood with no bacteria; imaging or cystoscopy is the next step when symptoms persist, especially over 50.
Symptoms that can go with it
- Burning on urination with vaginal or urethral discharge, itching or soreness, suggesting an STI or vaginitis
- Persistent bladder pressure, pain that eases after voiding and frequency lasting more than 6 weeks, typical of interstitial cystitis
- Blood in the urine without infection, which always needs explanation
- Flank pain that comes in waves, suggesting a stone
- Weight loss, night sweats or a long cough with sterile pyuria, which raise the question of tuberculosis
Read it alongside
- Bacteria in urine (microscopy) — a rapid, less specific indicator; many bacteria with white cells predicts a positive culture, bacteria without white cells predicts contamination.
- Leukocytes in urine and leukocyte esterase — pyuria supports a positive culture being a real infection; a positive culture without pyuria suggests contamination or colonization.
- Nitrite in urine — positive nitrite is highly specific for gram-negative bacteriuria and often predicts what the culture will grow.
- Squamous epithelial cells in urine — more than 5 per low-power field indicates a contaminated sample, and a mixed-flora culture usually follows.
- Blood in urine — common during infection; blood that persists on a repeat test after a negative culture needs further evaluation.
- White blood cell count, CRP and procalcitonin — raised in pyelonephritis and sepsis, normal in simple cystitis; blood cultures are added when there is fever.
- Chlamydia and gonorrhea tests — ordered when symptoms persist with a negative culture, particularly under 25 or with a new partner.
- Creatinine and eGFR — checked in pyelonephritis, obstruction or when choosing antibiotic doses.
What usually happens next
- A positive culture with symptoms is treated with an antibiotic the organism is sensitive to; if you were already started on one that is reported resistant and are not improving, expect a switch.
- A positive culture without symptoms in a non-pregnant adult is usually left alone; ask whether the test was needed before accepting treatment for it.
- Mixed flora or a contaminated sample is repeated as a careful midstream clean-catch sample delivered within 2 hours, or a catheter sample, rather than treated.
- A negative culture with ongoing symptoms leads to tests for chlamydia, gonorrhea and vaginal infection, a check for recent antibiotics, and, if white cells persist, imaging for stones and in older adults a cystoscopy.
- A follow-up culture to confirm clearance is not needed after symptoms resolve, except in pregnancy (and sometimes after kidney infection or in people with structural problems).
- Recurrent positive cultures (two in 6 months or three in a year) prompt a review of contraception, menopause, bladder emptying, prostate size, stones and diabetes, and a discussion of prevention options including vaginal estrogen, prophylactic antibiotics or methenamine.
Diet, lifestyle and natural levers with evidence
What can move Urine C&S once the cause is known. Nothing here replaces finding the cause.
Collection technique and prompt delivery (what most changes a culture result)
Moderate evidenceNothing dietary or herbal alters a culture, but how the sample is taken does. Around 30 percent of midstream samples from women are contaminated; a trial of 242 women found cleansing made no difference (32 percent contaminated with cleansing, 29 percent without), while holding the labia apart, catching the midstream and delivering the sample within 2 hours or refrigerating it do reduce false-positive and mixed-flora results. In infants, bag samples are contaminated so often that catheter samples are standard before treatment.
Higher water intake for recurrent cystitis
Strong evidenceIn a 12-month randomized trial of 140 premenopausal women with recurrent cystitis who drank less than 1.5 liters a day, adding 1.5 liters of water a day reduced culture-confirmed cystitis episodes from 3.2 to 1.7 per year and antibiotic courses by a similar proportion. More frequent voiding flushes bacteria before they reach significant counts. No benefit has been shown in people who already drink normally.
Cranberry products for prevention
Moderate evidenceThe 2023 Cochrane review of 50 randomized trials found cranberry juice, capsules or tablets reduced symptomatic, culture-verified urinary infections by about 26 percent in women with recurrent infections and by roughly half in children and after bladder procedures, with no benefit in care-home residents, pregnant women or people with bladder-emptying problems. Cranberry prevents attachment of E. coli; it does not treat a positive culture or clear asymptomatic bacteriuria.
Can potentiate warfarin; juice adds sugar and oxalate, so capsules are preferred for people with calcium oxalate stones.
D-mannose for prevention
Preliminary evidenceA 2014 trial of 308 women reported recurrence in 15 percent on 2 g of D-mannose daily versus 61 percent with no prophylaxis over 6 months, but the 2024 MERIT trial of 598 women in UK general practice found no difference from placebo (51 versus 55 percent with a further medically attended infection). It is safe but the evidence is now mixed.
Vaginal lactobacillus and, after menopause, asking about vaginal estrogen
Preliminary evidenceAn intravaginal Lactobacillus crispatus product reduced recurrence to 15 percent versus 27 percent with placebo in a 100-woman randomized trial, while oral probiotics have shown inconsistent results and no clear benefit in a Cochrane review. Low-dose vaginal estrogen, a prescription rather than a supplement, reduced recurrent infections in postmenopausal women from about 6 to 0.5 episodes per year in a landmark trial by restoring lactobacilli and acidic pH, and is worth raising with your clinician.
When to see a clinician promptly
- Fever above 100.4°F (38°C), shaking chills, flank pain or vomiting with urinary symptoms, whether or not the culture is back: possible pyelonephritis, same-day assessment; go to an emergency department if you cannot keep fluids down.
- Confusion, a heart rate over 100, fast breathing, low blood pressure or feeling faint with a suspected urinary infection: signs of urosepsis, an emergency.
- A positive culture reported resistant to the antibiotic you are taking, especially if you are not improving after 48 hours.
- Any positive culture, or any urinary symptoms, in pregnancy, in a man, in a child, in someone with a catheter, kidney transplant, diabetes or a weakened immune system.
- Symptoms that persist after a negative culture, or that return within 2 weeks of treatment.
- Blood in the urine that remains after infection is excluded or treated, particularly over age 50 or in smokers.
Frequently asked questions
What is a normal urine culture result?
No growth after 24 to 48 hours, or fewer than 10,000 CFU/mL of mixed skin and genital organisms, which many labs report as 'no significant growth' or 'normal urogenital flora'. A normal culture means no typical bacterial urinary infection was found. If you still have symptoms, other causes such as chlamydia, vaginitis, recent antibiotics or a low-count infection below the lab's reporting threshold are considered.
What does 100,000 CFU/mL mean on a urine culture?
It means 100,000 colony-forming units of bacteria grew from each milliliter of urine, written as 10^5 or 'greater than 100,000'. This is the traditional threshold for significant bacteriuria: with urinary symptoms it confirms infection; without symptoms it is asymptomatic bacteriuria, which is common and not treated except in pregnancy or before urological procedures. The organism's name and antibiotic sensitivities are reported with it.
What does mixed flora on a urine culture mean?
Two or more different species grew, usually each at low counts, and no single one dominates. In almost every case this means the sample picked up bacteria from the skin, vagina or foreskin during collection, or sat too long before being plated, so the lab does not run sensitivities. It does not mean you have several infections. If you have symptoms, repeat the test with a careful midstream clean-catch or catheter sample.
How long does a urine culture take?
Plates are read after 18 to 24 hours of incubation. A negative result is usually reported at 24 to 48 hours; a positive result gets a preliminary report (organism growing, approximate count) at 24 to 48 hours and the final identification with antibiotic sensitivities at 48 to 72 hours. Slow-growing or unusual organisms, fungi and tuberculosis cultures take longer, from several days to weeks.
Can a urine culture be positive without an infection?
Yes. Asymptomatic bacteriuria, bacteria living in the bladder without causing symptoms, is found in up to 5 percent of healthy young women, up to 20 percent of women over 80, half of nursing-home residents and virtually everyone with a long-term catheter. It is a positive culture but not an infection, and treating it does not prevent future infections. Contamination during collection can also produce a positive-looking count, usually of several species.
What do S, I and R mean on the sensitivity report?
S (sensitive or susceptible) means the organism is inhibited by achievable doses of that antibiotic, so it should work. R (resistant) means it will not. I (intermediate) means it may work at higher doses or in the urine, where many antibiotics concentrate. Some reports also give the MIC, the lowest drug concentration that stopped growth; a lower MIC relative to the breakpoint is better. Your clinician chooses the narrowest-spectrum S option that suits you.
Can I have a urine infection with a negative culture?
Occasionally. Standard labs may not report counts below 1,000 or 10,000 CFU/mL, yet bladder counts of 100 to 1,000 cause real symptoms in some women; antibiotics taken before the sample can also suppress growth. If your symptoms are typical and the dipstick shows white cells, many clinicians treat anyway. Persistent symptoms with repeatedly negative cultures point instead to urethritis from an STI, vaginitis, interstitial cystitis or a stone.
Do I need a repeat urine culture after antibiotics?
Not if your symptoms have resolved and you are not pregnant; a follow-up culture in healthy adults often shows asymptomatic bacteriuria that then gets treated unnecessarily. In pregnancy a repeat culture is standard, and it is sometimes done after pyelonephritis, in people with stones, catheters or structural abnormalities, or when symptoms did not fully clear.
References
- Urine culture. MedlinePlus, US National Library of Medicine (2023)View source
- Bacterial urinary tract infections. Merck Manual Professional Version (2024)
- Gupta K, Hooton TM, Naber KG, et al.. International clinical practice guidelines for the treatment of acute uncomplicated cystitis and pyelonephritis in women: a 2010 update by the Infectious Diseases Society of America and the European Society for Microbiology and Infectious Diseases. Clinical Infectious Diseases (2011)
- Nicolle LE, Gupta K, Bradley SF, et al.. Clinical practice guideline for the management of asymptomatic bacteriuria: 2019 update by the Infectious Diseases Society of America. Clinical Infectious Diseases (2019)
- Hooton TM, Roberts PL, Cox ME, Stapleton AE. Voided midstream urine culture and acute cystitis in premenopausal women. New England Journal of Medicine (2013)
- Stamm WE, Counts GW, Running KR, et al.. Diagnosis of coliform infection in acutely dysuric women. New England Journal of Medicine (1982)
- Wilson ML, Gaido L. Laboratory diagnosis of urinary tract infections in adult patients. Clinical Infectious Diseases (2004)
- Lifshitz E, Kramer L. Outpatient urine culture: does collection technique matter?. Archives of Internal Medicine (2000)
- Hooton TM, Bradley SF, Cardenas DD, et al.. Diagnosis, prevention, and treatment of catheter-associated urinary tract infection in adults: 2009 international clinical practice guidelines from the Infectious Diseases Society of America. Clinical Infectious Diseases (2010)
- Simerville JA, Maxted WC, Pahira JJ. Urinalysis: a comprehensive review. American Family Physician (2005)
- Hooton TM, Vecchio M, Iroz A, et al.. Effect of increased daily water intake in premenopausal women with recurrent urinary tract infections: a randomized clinical trial. JAMA Internal Medicine (2018)
- Williams G, Stothart CI, Hahn D, et al.. Cranberries for preventing urinary tract infections. Cochrane Database of Systematic Reviews (2023)
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