If the antibiotic I want to use is not reported on the urine culture susceptibility panel for a patient with an uncomplicated urinary tract infection, what should I do?

What to Do When Your Desired Antibiotic Is Not Listed on the Urine Culture Susceptibility Panel

Contact the microbiology laboratory to request susceptibility testing for the specific antibiotic you want to use, as laboratories routinely test only a limited panel of antibiotics but can perform additional testing on the stored isolate. 1

Understanding Why Antibiotics Are Missing from Reports

Microbiology laboratories do not test every available antibiotic against each isolate—they report a selective panel based on:

• Clinical relevance for the infection site (urinary tract)
• Antimicrobial stewardship principles (avoiding unnecessary broad-spectrum agents)
• Local resistance patterns and formulary preferences 2

The laboratory retains the bacterial isolate for several days and can perform supplemental susceptibility testing upon request from the treating clinician. 1

Step-by-Step Approach When Your Antibiotic Is Not Reported

Step 1: Verify the Antibiotic Is Appropriate for Uncomplicated UTI

Before requesting additional testing, confirm your chosen antibiotic is guideline-recommended for uncomplicated cystitis:

• First-line agents: Fosfomycin trometamol (3g single dose), nitrofurantoin (100mg twice daily for 5 days), or pivmecillinam (400mg three times daily for 3-5 days) 2
• Alternative agents: Trimethoprim-sulfamethoxazole (160/800mg twice daily for 3 days) if local resistance <20%, or cephalosporins (e.g., cefadroxil 500mg twice daily for 3 days) if local E. coli resistance <20% 2

Critical pitfall: Avoid requesting testing for antibiotics with poor urinary penetration or those inappropriate for uncomplicated UTI (e.g., doxycycline, which lacks adequate activity against common uropathogens causing cystitis). 1

Step 2: Call the Microbiology Laboratory

Contact the laboratory directly and request:

• Specific susceptibility testing for your desired antibiotic
• Minimum inhibitory concentration (MIC) if available, particularly for borderline organisms 1
• Turnaround time (typically 24-48 hours for additional testing)

The laboratory can test the stored isolate without requiring a new urine specimen. 1

Step 3: Use Empiric Therapy While Awaiting Results

If the patient requires immediate treatment and you're awaiting supplemental susceptibility data:

• Choose empiric therapy based on reported susceptibilities from the existing culture panel 2
• Select an agent with demonstrated susceptibility rather than waiting for testing of your preferred antibiotic 2
• Reassess therapy at 48-72 hours once supplemental testing is available 1

The choice of antimicrobial therapy should be guided by the spectrum and susceptibility patterns of the aetiological pathogens, efficacy for the particular indication in clinical studies, tolerability and adverse reactions, adverse ecological effects, and costs/availability. 2

Step 4: Consider Class-Based Susceptibility Predictions

For certain antibiotic classes, you can make reasonable inferences about susceptibility:

• Within fluoroquinolones: If ciprofloxacin is reported as susceptible, levofloxacin will typically also be effective (though cross-resistance can occur) 1
• Within beta-lactams: Susceptibility to one cephalosporin generation does not guarantee susceptibility to others—request specific testing 1
• Trimethoprim-sulfamethoxazole: Cannot be predicted from other agents—requires direct testing 3, 4

Do not assume cross-susceptibility without microbiologic confirmation, particularly in patients with prior antimicrobial exposure or complicated UTI. 5

When Additional Testing Is Not Necessary

You may not need supplemental susceptibility testing if:

• The patient is clinically improving on an alternative agent from the reported panel after 48-72 hours 2, 1
• A first-line agent shows susceptibility on the existing report (e.g., nitrofurantoin, fosfomycin) 2
• Your desired antibiotic is not guideline-recommended for uncomplicated UTI (e.g., amoxicillin alone, which has high resistance rates) 1

Special Considerations for Recurrent or Treatment-Failure Cases

If symptoms do not resolve or recur within 2-4 weeks after treatment completion:

• Obtain a new urine culture with susceptibility testing rather than relying on the previous isolate 2
• Assume the infecting organism is not susceptible to the agent originally used 2
• Retreat with a 7-day regimen using a different agent based on the new culture results 2

For women whose symptoms do not resolve by the end of treatment, and for those whose symptoms resolve but recur within 2 weeks, a urine culture and antimicrobial susceptibility testing should be performed. 2

Common Pitfalls to Avoid

• Do not use antibiotics empirically without culture guidance in complicated UTI, as resistant organisms are more common and prior antimicrobial exposure increases resistance risk 5, 4
• Do not treat asymptomatic bacteriuria discovered incidentally on culture—this promotes resistance without clinical benefit 2, 1
• Do not assume susceptibility based on prior cultures from weeks or months earlier, as resistance patterns can change rapidly 5
• Do not use fluoroquinolones empirically if local resistance exceeds 10% or the patient has recent fluoroquinolone exposure 1

When to Obtain Urine Culture in Uncomplicated Cystitis

Routine urine culture is not indicated for typical uncomplicated cystitis in women with classic symptoms. 2 However, culture is recommended in:

• Suspected acute pyelonephritis (fever, flank pain, systemic symptoms) 2
• Symptoms that do not resolve or recur within 4 weeks after treatment completion 2
• Women with atypical symptoms or diagnostic uncertainty 2
• Pregnant women with any UTI symptoms 2
• Men with UTI symptoms (all male UTIs are considered complicated) 1

In patients presenting with typical symptoms of uncomplicated cystitis, urine analysis (urine culture, dipstick testing) leads to only a minimal increase in diagnostic accuracy. 2