Urine Cultures: Interpretations

Urine cultures are a fundamental diagnostic tool in clinical microbiology, used primarily to detect and identify pathogens responsible for urinary tract infections (UTIs). UTIs are among the most common bacterial infections encountered in clinical practice, affecting millions of individuals annually, with a higher incidence in women, the elderly, and individuals with underlying medical conditions. Here lies a detailed examination of urine cultures, focusing on the incidence and significance of various pathogens, including Escherichia coli, Klebsiella, Proteus, Pseudomonas aeruginosa, Enterococcus species, group B Strep (aka Streptococcus agalactiae), Staphylococcus saprophyticus, and Staphylococcus aureus.

The Importance of Urine Cultures

Urine cultures are performed when a UTI is suspected based on clinical symptoms, such as dysuria, frequency, urgency, and suprapubic pain, or when a patient presents with non-specific symptoms, such as fever or altered mental status, particularly in elderly patients. The goal of urine cultures is to isolate and identify the causative organism, allowing for targeted antimicrobial therapy. This is crucial, given the rising concern over antimicrobial resistance, which makes empirical treatment increasingly challenging.

The Standard Methodology of Urine Cultures

Urine samples for culture are typically collected through clean-catch midstream urine collection, catheterization, or suprapubic aspiration (uncommon). The sample is then inoculated onto culture media, such as blood agar and MacConkey agar, and incubated at 35-37°C for 18-24 hours. The growth of bacteria is quantified, with a colony count of 10^5 CFU/mL generally considered indicative of a significant infection, though lower counts may be clinically relevant in symptomatic patients.

Once growth is observed, the colonies are identified using a combination of biochemical tests, mass spectrometry (MALDI-TOF), or molecular techniques. In smaller labs, the identifications are done by a combination of benchtop biochemical tests (indole, oxidase, catalase, etc.) automated analyzers, whereas many larger laboratories have MALDI-TOF analyzers for quick day-of ID of most organisms. The pathogens are then subjected to antimicrobial susceptibility testing by plate testing (Kirby-Bauer) or automated panels to guide appropriate treatment.

The plates that a laboratory uses for urine culture work-up can vary by laboratory, but common plates used are as follows:

Blood agar plate (also known as BA or BAP): This will grow all organisms commonly worked up in UTIs. It is also helpful to determine the hemolysis pattern of colonies.

MacConkey plate (commonly called MAC): This plate is selective to grow only gram-negative organisms, making it extremely useful in urine cultures, where gram-negative organisms are the most common pathogens.

Chromogenic agars specifically designed for urine cultures may help with differentiating organisms commonly isolated in UTIs, especially for inexperienced techs.

Bile esculin agar (BEA) plates can help identify Enterococcus. Enterococcus species turn bile esculin agar black for easy identification.

Note: Gram stains directly from urine specimens are generally not performed routinely. 

General Rules for Working up Organisms in Urine Culture

Keep in mind, many patients have a combination of pathogens present in a urine culture. But most UTIs will be E. coli.

Work up all gram-negative rods unless it is determined that it is a bad collection (very mixed culture). This means, whatever grows pure on the MacConkey plate is likely to be a pathogen (unless it's a bad collection!)

Work up Enterococcus. This presents as a small gray colony on the blood plate, often alpha-hemolytic like many alpha-hemolytic Strep species. An easy way to rule in Enterococcus is to run a spot PYR test. Enterococcus is PYR positive, while other alpha-hemolytic streps are PYR negative.

Look for beta-hemolysis on the blood plate. These are either Staph aureus, beta-hemolytic streps, or gram-negative rods such as E. coli or Pseudomonas. These should be worked up.

Work up any traditional gram-positive pathogens such as Staph saprophyticus if the culture is not a bad collection.

Yeast. Yeasts are usually identified as either Candida albicans or Candida species (not albicans). The clinical significance is that Candida albicans is almost always susceptible to common anti-fungal agents.

Incidence and Significance of Common Pathogens

Escherichia coli (E. coli)

Anyone on the urine culture bench will tell you, E. coli is most of what they are working up. Escherichia coli is the most common pathogen isolated in urine cultures, responsible for approximately 70-90% of all community-acquired UTIs. The predominance of E. coli is largely due to its ability to adhere to the uroepithelium via pili and fimbriae, facilitating colonization and infection. E. coli is a Gram-negative rod that is part of the normal gut flora, and its transition from the gastrointestinal tract to the urinary tract often leads to infection. E. coli UTIs are typically straightforward to diagnose and treat, though increasing resistance to common antibiotics like trimethoprim-sulfamethoxazole and fluoroquinolones is a growing concern.

Klebsiella Species

Klebsiella species, particularly Klebsiella pneumoniae but also Klebsiella oxytoca, are responsible for about 5-10% of UTIs. These Gram-negative rods are also part of the gastrointestinal flora but are less commonly implicated in UTIs than E. coli. Klebsiella species possess a polysaccharide capsule that enhances their virulence by preventing phagocytosis and allowing them to evade the host immune response. Klebsiella UTIs are more commonly seen in hospitalized patients, particularly those with indwelling urinary catheters or other risk factors for complicated UTIs. The rise of extended-spectrum beta-lactamase (ESBL)-producing Klebsiella strains poses significant challenges in treatment, often necessitating the use of carbapenems or other advanced antibiotics.

Proteus Species

Proteus species, especially Proteus mirabilis and sometimes Proteus vulgaris account for 1-5% of UTIs. Proteus is a Gram-negative rod known for its ability to produce urease, an enzyme that hydrolyzes urea to ammonia, raising the pH of urine. This alkaline environment can lead to the formation of struvite stones, complicating the UTI and making treatment more difficult. Proteus UTIs are often associated with urinary tract abnormalities or catheterization. The bacterium's characteristic swarming motility on agar plates is a hallmark of its identification in the laboratory.

Pseudomonas aeruginosa

Pseudomonas aeruginosa is a Gram-negative bacterium that is occasionally isolated in urine cultures, particularly in patients with complicated urinary tract infections (UTIs). This pathogen is known for its ability to thrive in moist environments and is commonly associated with healthcare-associated infections, especially in individuals with indwelling urinary catheters, underlying urological abnormalities, or compromised immune systems. Pseudomonas UTIs can be challenging to treat due to the bacterium's intrinsic resistance to many common antibiotics, including beta-lactams and some fluoroquinolones. In urine cultures, Pseudomonas often grows on MacConkey agar, where it produces characteristic blue-green pigmented colonies due to the production of pyocyanin. Its presence in urine typically indicates a more severe infection that may require targeted antimicrobial therapy, often with agents such as piperacillin-tazobactam, ceftazidime, or carbapenems, depending on the sensitivity profile. The identification of Pseudomonas in urine cultures necessitates careful clinical evaluation to address the underlying risk factors and prevent potential complications.

Enterococcus Species

Enterococcus species, particularly Enterococcus faecalis and Enterococcus faecium, are Gram-positive cocci responsible for 5-10% of UTIs, especially in hospitalized patients. These bacteria are part of the normal intestinal flora and can cause infections when they translocate to the urinary tract. Enterococcus species are particularly challenging due to their intrinsic resistance to many antibiotics, including cephalosporins and low-level resistance to aminoglycosides. The rise of vancomycin-resistant enterococci (VRE) is a significant concern in healthcare settings, where these infections are often associated with high morbidity.

Group B Streptococcus (GBS)

Group B streptococcus (Streptococcus agalactiae) is a Gram-positive coccus that is a notable cause of UTIs in pregnant women, diabetics, and the elderly. While GBS is most commonly associated with neonatal infections, it can also cause asymptomatic bacteriuria and symptomatic UTIs in adults. GBS bacteriuria in pregnant women is particularly concerning because it can lead to neonatal sepsis, necessitating screening and treatment during pregnancy. The incidence of GBS in urine cultures is less than 5%, but its presence is clinically significant, especially in vulnerable populations.

Staphylococcus saprophyticus

Staphylococcus saprophyticus is a coagulase-negative staphylococcus and a common cause of UTIs in young, sexually active women, accounting for 5-10% of cases. Unlike E. coli, S. saprophyticus is not part of the normal gut flora but is instead a colonizer of the skin and genitourinary tract. Infections with S. saprophyticus are typically less severe than those caused by E. coli, and the bacterium is generally sensitive to a wide range of antibiotics. However, its presence in urine cultures is clinically significant due to its specific association with UTIs in this demographic.

Staphylococcus aureus

Staphylococcus aureus is a Gram-positive coccus that is a relatively uncommon cause of UTIs, accounting for less than 5% of cases. When S. aureus is isolated in urine cultures, it often suggests hematogenous spread rather than ascending infection, indicating a possible underlying infection elsewhere in the body. This makes S. aureus bacteriuria a potential marker for more serious conditions, such as endocarditis. Methicillin-resistant Staphylococcus aureus (MRSA) further complicates the treatment of these infections, necessitating the use of alternative antibiotics such as vancomycin or linezolid.

Other organisms

Many other organisms can cause UTI, including other enterics such as Citrobacter and Enterobacter, and other gram-positives such as Staphylococcus epidermidis and group A strep. It is important to note that any organism can be pathogenic, especially in elderly and immune-deficient populations and every lab should have a written algorithm for what quantities constitute an infection. >100,000 CFUs/mL is generally considered a clear infection if pure, but different populations will require different rules and should be built in collaboration with the Medical Laboratory Director, the provider team, and pharmacy.

Common Antibiotic Therapy for Urinary Tract Infections

First-Line Antibiotic Therapies

Uncomplicated UTIs will generally be managed empirically.

Nitrofurantoin

Nitrofurantoin is a commonly prescribed first-line antibiotic for uncomplicated UTIs, particularly acute cystitis in women. It is highly effective against the most common UTI pathogen, Escherichia coli, as well as other Gram-negative bacteria and some Gram-positive organisms like Enterococcus. Nitrofurantoin's mechanism of action involves disrupting bacterial cell wall synthesis, leading to cell death. The drug is well-tolerated and has minimal systemic side effects because it concentrates in the urine, which is ideal for treating lower UTIs. However, it is not effective for upper urinary tract infections, such as pyelonephritis, due to its poor tissue penetration. The typical course of nitrofurantoin is 5-7 days, with a common dosage of 100 mg taken twice daily.

Trimethoprim-Sulfamethoxazole (TMP-SMX)

Trimethoprim-sulfamethoxazole (TMP-SMX), also known as co-trimoxazole, is another first-line therapy for uncomplicated UTIs. This combination antibiotic inhibits bacterial folic acid synthesis, leading to a bactericidal effect. TMP-SMX is effective against a broad spectrum of UTI pathogens, including E. coli, Klebsiella, and Proteus species. However, the increasing prevalence of E. coli strains resistant to TMP-SMX has led to a decline in its use as a first-line therapy in some regions. When prescribed, TMP-SMX is typically given as a double-strength tablet (160 mg trimethoprim/800 mg sulfamethoxazole) taken twice daily for 3 days in uncomplicated cases. Despite its effectiveness, TMP-SMX is contraindicated in patients with sulfa allergies, and it can cause adverse reactions such as rash, gastrointestinal disturbances, and, rarely, hematologic abnormalities.

Fosfomycin

Fosfomycin is an antibiotic that has gained popularity as a first-line treatment for uncomplicated UTIs, especially in settings with high rates of antibiotic resistance. It works by inhibiting bacterial cell wall synthesis, which results in bacterial lysis. Fosfomycin has a broad spectrum of activity, including coverage against E. coli, Klebsiella, and Enterococcus species. One of its key advantages is its convenient dosing: a single 3-gram oral dose dissolved in water is typically sufficient to treat an uncomplicated UTI. This single-dose regimen enhances patient compliance and minimizes the risk of resistance development. Fosfomycin is generally well-tolerated, with the most common side effects being mild gastrointestinal symptoms. However, it is not recommended for use in pyelonephritis or complicated UTIs due to its limited tissue penetration.

Alternative Antibiotic Therapies

These are antimicrobials generally reserved for more difficult to treat UTIs.

Fluoroquinolones

Fluoroquinolones, such as ciprofloxacin and levofloxacin, have been widely used for the treatment of UTIs, particularly complicated cases and pyelonephritis. These antibiotics inhibit bacterial DNA gyrase and topoisomerase IV, leading to the disruption of DNA replication and cell death. Fluoroquinolones have excellent tissue penetration, making them effective against both lower and upper urinary tract infections. However, due to increasing resistance rates and concerns about their side effects—such as tendinitis, tendon rupture, and potential central nervous system toxicity—the use of fluoroquinolones as first-line therapy for uncomplicated UTIs has declined. They are now typically reserved for more severe infections or when other antibiotics are contraindicated. The usual dosage for uncomplicated UTIs is 250-500 mg of ciprofloxacin or 250 mg of levofloxacin once or twice daily for 3 days.

Beta-lactams

Beta-lactam antibiotics, including amoxicillin-clavulanate, cefdinir, cefpodoxime, and cefuroxime, are often used as alternative treatments for UTIs. These antibiotics inhibit bacterial cell wall synthesis, leading to cell lysis and death. Beta-lactams are effective against a wide range of UTI pathogens, but they are generally less preferred as first-line therapy due to their lower efficacy compared to nitrofurantoin, TMP-SMX, and fosfomycin. However, they are an important option for patients with allergies to other antibiotics or when resistance patterns dictate their use. The typical treatment course involves a 5-7 day regimen, with dosages varying depending on the specific beta-lactam used.

Aminoglycosides

In cases of severe or complicated UTIs, aminoglycosides like gentamicin and amikacin may be used, often in combination with other antibiotics. These drugs inhibit bacterial protein synthesis and are particularly effective against gram-negative bacteria, including multidrug-resistant strains. Due to their potential nephrotoxicity and ototoxicity, aminoglycosides are generally reserved for hospitalized patients with serious infections. They are typically administered intravenously, with dosing adjusted based on the patient's renal function and serum drug levels.

Considerations in Antibiotic Selection

The choice of antibiotic therapy for a UTI depends on several factors, including the severity and location of the infection (lower vs. upper urinary tract), the patient's allergy history, local resistance patterns, and the patient's renal function. In cases of uncomplicated cystitis, shorter courses of antibiotics (3-5 days) are usually sufficient, while more extended courses are necessary for complicated UTIs or pyelonephritis. Additionally, the increasing prevalence of antibiotic-resistant pathogens necessitates careful selection of therapy to ensure effectiveness while minimizing the risk of promoting further resistance. If the laboratory has any questions about antibiotic therapies or resistance testing, a quick call to the pharmacy is a sure bet.