13.2 Aseptic Processing, Storage, and Transport of Micro Specimens
Key Takeaways
- Never sniff culture plates; plate odors are an aerosol and laboratory-acquired-infection risk, not an identification method (AMT CMLA III.8.B.1).
- Routine clinical microbiology is typically Biosafety Level 2 (BSL-2) work; treat plates, fluids, and used loops as biohazard.
- Amies or similar transport keeps bacterial swabs moist; blood-culture bottles are the blood specimen; anaerobes need anaerobic containers, not a dry aerobic swab.
- Do not refrigerate inoculated blood-culture bottles; delayed urine cultures go refrigerated or into boric-acid preservative; stool transport follows the test ordered.
- Used loops, needles, and broken slides are sharps; dispose of micro waste per SOP in biohazard or sharps containers—not regular trash.
AMT III.8.B.1 requires special safety procedures and aseptic techniques for processing microbiological specimens. III.8.B.2 requires you to prepare, store, dispose of, and properly transport those specimens according to standard operating procedure. This is not a restage of Chapter 2 isolation theory. Microbiology adds live organisms that can aerosolize from plates, loops, and bubbling bottles. A CMLA who processes micro specimens is handling other potentially infectious materials (OPIM) under the Occupational Safety and Health Administration (OSHA) Bloodborne Pathogens Standard and the laboratory’s biosafety procedures.
Quick Answer: Treat plates as biohazard. Know Biosafety Level (BSL) awareness—clinical benches are typically BSL-2. Never sniff plates. Use aseptic technique. Keep swabs moist (Amies). Put blood into blood-culture bottles, not an SST. Anaerobes need anaerobic transport. Do not refrigerate inoculated blood-culture bottles. Delayed urine cultures go cold or into boric acid. Stool depends on the order. Loops and slides can be sharps.
Why microbiology safety is stricter than “wipe the chair”
A chemistry aliquot is usually sterile fluid. A micro plate is a lawn or colony of living organisms. Opening it on an open bench, centrifuging uncovered fluids, flaming a loop so it spatters, or sniffing “to see if it smells like Pseudomonas” can put organisms into your lungs. Historical laboratory-acquired infections include Neisseria meningitidis, Brucella, Mycobacterium tuberculosis, Salmonella, and dimorphic fungi. You do not need the case-report catalog. You need the habit: lid on, no smell test, no mouth pipetting, disinfect the bench, and process high-risk respiratory or mold work in the containment the SOP names—often a biological safety cabinet (BSC).
Biosafety Level is a CDC/NIH containment scale. Teaching awareness for CMLA:
| Level | Teaching idea | Clinical lab note |
|---|---|---|
| BSL-1 | Well-characterized agents not known to consistently cause disease in healthy adults | Not the default for patient specimens |
| BSL-2 | Agents associated with human disease; splash and sharps risk | Typical clinical microbiology bench |
| BSL-3 | Serious or lethal agents with aerosol transmission (example: M. tuberculosis cultures in many programs) | Specialized rooms; not a CMLA freelance bench |
You are not the biosafety officer. You are the person who does not open a powdery mold plate on the phlebotomy desk, does not centrifuge sputum without a sealed carrier if SOP requires it, and does not carry dripping plates through the waiting room.
Never sniff plates. Identification by odor is an outdated, dangerous teaching trick. Even “friendly” organisms can share a plate with something that infects. If a coworker says the grape smell confirms Pseudomonas, the exam answer is still do not sniff.
Aseptic processing at assistant level
Aseptic technique here means you do not add organisms to the specimen or to yourself. Practical CMLA moves:
- Work on a disinfected, uncluttered surface; wipe with the EPA-registered disinfectant the SOP names and observe wet-contact time.
- Personal protective equipment: gloves, lab coat or gown, and eye protection as the SOP lists; add a mask or respirator when the SOP requires it for AFB or aerosol procedures.
- Do not rest inoculated loops or swab sticks on the bench blotter.
- Open plates only as needed; keep lids over the agar like a shield, not a frisbee.
- Disposable loops are single-use. If the laboratory still uses reusable wire loops, they are sterilized in an incinerator or flame per SOP—and a hot loop that spatters is an aerosol event, not a shortcut. A cooling loop that you set down wrong is still a sharp if it can puncture a bag or a glove.
- Broken slides and coverslips from stains are sharps. Needles from blood-culture collection were already Chapter 3; they still go in a puncture-resistant container.
- Do not eat, drink, apply cosmetics, or handle contact lenses in the processing area.
If you splash a plate or a blood-culture bottle, follow the exposure-control plan (Chapter 3): wash or irrigate, report, and do not hide the spill because “it was only urine.”
Transport media: Amies, blood-culture bottles, anaerobic containers
A dry swab on the way to the laboratory is a dead or overgrown specimen. Transport media keep organisms alive (or at least recoverable) without letting them multiply into a fiction.
| System | What it is for | CMLA handling |
|---|---|---|
| Amies (with or without charcoal) | Bacterial swabs (throat, wound, some genital) | Keep the swab moist in the column; break or recap as the device is designed; do not leave it dry on the counter |
| Blood-culture bottles | Blood C&S | Inoculate the bottles; do not pour blood into a red-top and “make a culture later”; invert gently to mix; keep ambient; get them on the incubator path fast |
| Anaerobic vials, gassed-out tubes, or anaerobic transport swabs | Deep wounds, abscess aspirates, tissue for anaerobes | Air kills many anaerobes; a dry aerobic Amies swab is not a substitute when the order is anaerobic culture |
| Viral transport medium | Viruses | Not interchangeable with Amies unless the IFU says so |
| Enteric transport (for example Cary-Blair) | Stool culture | Different from O&P fixative and from a C. difficile cup (Chapter 9) |
Do not refrigerate or freeze a product the directory forbids. Do not inoculate blood-culture bottles with leftover lavender-top EDTA and call it a sterile collection.
Time and temperature: urine versus stool versus blood culture
One refrigerator is not a universal micro incubator.
| Specimen | Typical time/temperature teaching | Designed trap |
|---|---|---|
| Blood culture | Inoculate at collection; hold at room temperature; transport promptly to the laboratory for incubation; do not refrigerate inoculated bottles | Parking bottles in the specimen fridge “with the urines” delays detection and can injure some organisms |
| Urine culture | Unpreserved urine to the bench promptly—commonly within 2 hours at ambient; if delayed, refrigerate (about 2–8°C) or use a boric-acid preservative tube per SOP | Leaving a warm cup on the counter overnight overgrows flora and invents a “UTI” |
| Stool | Culture often uses enteric transport (Cary-Blair) held as the directory states (often ambient, timed). C. difficile testing commonly wants unformed stool, refrigerated, not in O&P fixative. O&P uses fill-to-the-line fixative vials | One stool cup is not every stool test |
| Throat/wound swab in Amies | Process as soon as possible; follow the labeled hold time and temperature | A 3-day dry swab in a drawer is a reject |
| CSF received for culture | STAT; do not treat it like leftover UA; many SOPs keep bacterial CSF culture at ambient and never discard volume (Chapter 9) | Fridge-then-forget |
Prepare means: right container, labeled, cap tight, biohazard bag, requisition matching the site and test. Store means: the temperature the directory names until processing. Dispose means: autoclave bags, sharps containers, and spill cleanup per SOP—plates do not go in the lunch-room trash.
Shipping follows the same Category B triple-packaging idea as other send-outs (Chapter 8/9): leak-tight primary, absorbent, secondary, rigid outer, biohazard marking, and a temperature pack that matches the reference-lab list. Blood-culture bottles and anaerobic vials are still biohazard, not regular mail.
Scenario
A courier drops a bag: two blood-culture bottles packed in ice “because everything infectious is cold,” a urine cup collected 6 hours ago sitting warm, and a wound swab that pulled out of Amies and dried. Do not load the bottles into the fridge to “keep the ice theme.” Notify the laboratory, document the temperature abuse, and reject or recollect the urine and the dry swab per SOP. Blood-culture bottles that were iced contrary to SOP are a documented problem, not a silent load.
Exam traps
- Sniffing plates to identify organisms.
- Refrigerating inoculated blood-culture bottles.
- Treating a dry swab as equivalent to Amies or anaerobic transport.
- Using one stool kit for culture, O&P, and C. difficile.
- Tossing loops and slides in regular trash.
- Processing a powdery mold plate at the open phlebotomy bench.
Keep it alive only in the container designed for that organism, at the temperature designed for that test, without inhaling it.
While processing a blood-agar plate, a coworker suggests sniffing the growth to confirm Pseudomonas. What should the CMLA do?
Which time and temperature practice matches common microbiology SOP teaching?
A deep-abscess anaerobic culture and a throat culture are ordered. Which transport choice is correct?