Clinical microbiology

Why it matters

When someone has a serious infection, two questions drive treatment: what organism is it, and which antibiotics will work. The clinical microbiology lab answers both. Its reports look different from chemistry reports: organism names, colony counts and tables of MICs with S, I and R letters. An MLS has to produce those reports accurately and explain what each part means to the care team.

Safety and scope. Clinical microbiology is done in a biosafety level 2 (or higher) laboratory, under supervision, with training in biosafety and bloodborne pathogens (CDC BMBL, checked on 2026-10-23). Never attempt to culture anything at home. Choosing a treatment is the prescriber's decision; nothing here is medical advice.

The workflow

1. Specimen: blood culture bottles, urine, sputum, wound swab, spinal fluid. Quality matters: a sputum with many squamous epithelial cells is mostly saliva and may be rejected.
2. Direct examination: a Gram stainA direct stain that sorts bacteria into Gram-positive (purple) and Gram-negative (pink) and shows their shape and arrangement. sorts bacteria into Gram-positive (purple, thick peptidoglycan wall) and Gram-negative (pink) and describes shape (cocci, rods) and arrangement (clusters, chains). For a positive blood culture, this first result is phoned to the care team quickly.
3. Culture: the specimen is plated on media such as blood agar (general growth, hemolysis patterns), chocolate agar (fastidious organisms) and MacConkey agar (Gram-negative rods; lactose fermenters turn pink). Plates incubate, usually overnight.
4. Identification: biochemical tests, automated panels, or MALDI-TOFMass spectrometry that identifies an organism from its protein fingerprint in minutes. mass spectrometry, which identifies an organism from its protein fingerprint in minutes. Molecular panels (PCR) can identify organisms and some resistance genes directly from positive blood cultures.
5. Antimicrobial susceptibility testing (AST): measures whether antibiotics inhibit the organism.
6. Report: preliminary results are released as they become available, then a final report.

How susceptibility is measured

• Broth microdilution finds the minimum inhibitory concentrationMIC: the lowest antibiotic concentration in a doubling series that prevents visible growth. (MIC): the lowest antibiotic concentration (in a doubling series such as 0.5, 1, 2, 4, 8 ug/mL) that prevents visible growth.
• Disk diffusion places antibiotic disks on a lawn of the organism; the diameter of the clear zone of inhibition is measured in millimeters.

The MIC or zone size is then compared with breakpointsPublished cut-offs (CLSI, EUCAST) that turn an MIC or zone size into S, I/SDD or R for a given organism and drug. published by standards bodies (CLSI in the US, EUCAST in Europe) to give an interpretive category: S (susceptible), I or SDD (intermediate, or susceptible-dose-dependent), or R (resistant). Breakpoints are specific to the organism, the antibiotic and sometimes the infection site, and they are updated, which is why labs follow the current published edition rather than memorizing them.

Worked example: reading a report

A fictional urine culture report:

Specimen: Urine, clean catch
Culture: >100,000 CFU/mL Escherichia coli
Susceptibility (MIC, ug/mL):
  Ampicillin            >16   R
  Cefazolin              2    S
  Nitrofurantoin        <=16  S
  Trimethoprim/sulfa    >2/38 R
  Ciprofloxacin          0.25 S

How to read it:

• CFU/mL is the colony count. Interpretation depends on the specimen and collection method, so the source line matters.
• An MIC number is meaningful only with its interpretation; you cannot compare MIC numbers across different antibiotics to pick "the strongest" one, because each drug has its own breakpoint.
• Many labs use cascade reportingSuppressing broader-spectrum drugs on a report when narrower ones test susceptible, to support antimicrobial stewardship.: broader-spectrum drugs are suppressed when narrower ones test susceptible, to support antimicrobial stewardship. A missing drug may be deliberate.
• Some organisms have intrinsic resistanceResistance an organism naturally has to a drug, so the drug is not tested or is reported resistant automatically. (for example many Gram-negative rods to vancomycin), so those drugs are not tested or are reported as resistant automatically.

Common mistakes

• Comparing MIC values between different antibiotics as if lower always means better.
• Ignoring the specimen source when reading colony counts.
• Treating a mixed growth of several skin or urogenital organisms as a single pathogen (often it signals contamination and a recollection).
• Using outdated breakpoint tables.

Quick recap

• Workflow: specimen, Gram stain, culture, identification (often MALDI-TOF), susceptibility, report.
• MIC = lowest concentration that inhibits growth; disk diffusion measures zone diameter.
• Breakpoints from CLSI or EUCAST turn MICs and zones into S, I/SDD or R.
• Cascade reporting and intrinsic resistance explain why some drugs are missing from a report.

Try it

Open the Do tab for the quiz: read a culture and susceptibility report.