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Wise Use of Antibiotics

December 2021

Decoding Microbiology Results: Clinical Applications of Culture and Susceptibilities


Author: Alaina Burns, PharmD, BCPPS | Clinical Pharmacy Specialist, Infectious Diseases and Antimicrobial Stewardship


Column Editor: Rana El Feghaly, MD, MSCI | Director, Clinical Services | Director, Outpatient Antibiotic Stewardship Program | Associate Professor of Pediatrics, UMKC School of Medicine


Making the correct diagnosis is an essential step to promoting optimal antimicrobial use.1 One resource often used to make a diagnosis is microbiology tests, such as cultures and susceptibilities. However, interpreting these results clinically is not always intuitive. The following microbiology considerations can help clinicians use microbiology results to optimize antimicrobial prescribing.

Are microbiology cultures always indicated to facilitate diagnosis?

As available diagnostic tests have increased, so has reliance on these tests to help diagnose patients. While microbiological testing is often viewed as an objective measure supporting an infectious diagnosis, obtaining cultures in low-yield settings or in cases where cultures are not needed may lead to confusing situations. For example, what should we do with growth of a multidrug-resistant organism from a wound culture when a patient’s symptoms have resolved without treating it?2 How should we interpret a blood culture obtained from a child with community-acquired pneumonia now growing Streptococcus mitis? What should we make of a throat culture obtained from a child with upper respiratory symptoms now growing Pseudomonas aeruginosa? Taking time to question whether a culture will add value to your workup is the first step in shifting away from the “culture of culturing.”

Does positive microbial growth on cultures always need to be treated?

While cultures are invaluable tools for identifying pathogens, a common misconception is that any microbial growth indicates an infection requiring treatment. The first question should therefore be “Does this represent colonization, contamination or infection?” The need to ask this question is particularly important when dealing with nonsterile sites such as wounds or the respiratory tract. Treating colonization or contamination leads to unnecessary antimicrobial courses and increases the risk of patient harm. By taking time to consider how the results relate to the patient’s clinical picture, prescribers can combat the tendency to misinterpret culture results.2

One way our microbiology laboratory works to mitigate misinterpretations is by refraining from reporting irrelevant organisms,3 such as reporting only beta-hemolytic streptococci from throat cultures or true pathogens from stool cultures.

Alternatively, a culture that returns with no growth does not always indicate that a patient does not have a bacterial infection. Pre-treated culture is one prime example here. In these cases, considering the most likely pathogens and which of those were likely covered by the prior antibiotic may be helpful in directing further therapy.

Does the collection method play a role in microbiology interpretation?

Appropriate culture collection techniques are essential to decrease the risk of contamination. For example, using pedi-bags for urine culture in infants significantly increases the risk of contamination with gastrointestinal and skin flora; thus, guidelines recommend catheterized specimens in patients unable to provide a clean catch. An accurate collection technique also increases the chances of recovering the causative agent. For example, obtaining anaerobic cultures is the only way to identify infections caused by anaerobic bacteria that would otherwise be missed in certain circumstances.

When should therapy be changed based on early microbiology results?

A gram stain can facilitate clinical decision-making. In general, therapy may be broadened based on a gram stain result but should typically not be narrowed.4 Rapid diagnostics may allow for streamlining antimicrobial therapy; rapid antigen tests (viral, streptococcal pharyngitis) may help with antibiotic initiation decisions. Newer technologies such as the BioFire Blood Culture Identification Panel (BCID) or mass spectrometry now allow for faster identification of organisms, helping streamline therapy. Another example is the penicillin-binding protein 2A (PBP2a) test, which helps identify methicillin-resistant Staphylococcus aureus quickly, rather than wait for complete susceptibilities. Using this test, then, may de-escalate treatment from clindamycin to cephalexin a day earlier if PBP2a is negative.5

Antimicrobial susceptibilities: What agent is best for my patient?

Antimicrobial susceptibilities help providers identify optimal agents to treat pathogens. Breakpoints take into consideration antibiotic dosing, clinical indications, sites of infections, and the specific organisms.6 An interpretation of "susceptible" means the antibiotic is effective at standard doses. In cases where the interpretation is "susceptible dose dependent (SDD)" or "intermediate (I)," therapeutic success can likely be obtained by using higher doses or modified dosing strategies. In these cases, consultation with an infectious diseases specialist or pharmacist is encouraged. 

A common misconception with susceptibilities is clinical interpretations of the minimum inhibitory concentration (MIC). The MIC is simply the lowest antibiotic concentration preventing visible bacterial growth in a test tube. This value alone does not predict therapeutic success in patients; thus, one should not assume the antibiotic with the lowest MIC is the most effective. Instead, when selecting an antibiotic from a susceptibility report, providers should consider antibiotics that reach the site of infection effectively and have clear pediatric dosing for the indication.

Overall, microbiology results can serve as an important resource for optimizing antimicrobial prescribing. While culture results can provide objective data, assessing the result using the entire clinical picture is essential for optimal use of these diagnostic tools.



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  2. Vaughn VM, Szymczak JE, Newton DW, Fakih MG. Addressing the overuse of cultures to optimize patient care. Ann Intern Med. 2019;171:S73-S74.
  3. Miller JM, Binnicker MJ, Campbell S, et al. A guide to utilization of the microbiology laboratory for diagnosis of infectious diseases: 2018 update by the Infectious Diseases Society of America and the American Society for Microbiology. Clin Infect Dis. 2018;67(6):e1-e94.
  4. Giuliano C, Patel CR, Kale-Pradhan PB. A guide to bacterial culture identification and results interpretation. P T. 2019;44(4):192-200.
  5. O’Donnell LA, Guarascio AJ. The intersection of antimicrobial stewardship and microbiology: educating the next generation of health care professionals. FEMS Microbiol Lett. 2017;364(1):1-7.
  6. Kowalska-Krochmal B, Dudek-Wicher R. The minimum inhibitory concentration of antibiotics: methods, interpretation, clinical relevance. Pathogens. 2021;10(2):165. doi:10.3390/pathogens10020165