Lecture -6
Title: Laboratory Methods: Collection and Handling of Clinical Specimens,
and Identification of Pathogenic Organisms
1. Importance of Proper Specimen Collection, Transport, and Processing
Accurate diagnosis of infectious diseases heavily depends on the quality of clinical
specimens and the procedures followed from collection to laboratory analysis, improper
specimen handling can result in misdiagnosis, treatment failure, and increased
transmission of infectious agents.
Explain the importance of proper specimen collection, transport, and processing in
diagnosing infectious diseases.
Highlight the role of medical professionals in ensuring diagnostic accuracy.
1.1. Specimen Collection
Key Principles:
Timing: Collect specimens prior to the administration of antimicrobial agents, which
may suppress or eliminate the pathogen.
Site Selection: Collect from the actual site of infection, avoiding contamination from
skin, mucous membranes, or environmental sources.
Sterility: Use aseptic technique to prevent introduction of external organisms.
Quantity: Collect an adequate volume based on the test required (e.g., 20 mL for
adult blood cultures).
Labeling and Documentation: Each specimen must be properly labeled with:
o Patient name and ID
o Date and time of collection
o Type of specimen and anatomical site
o Clinical information (symptoms, suspected diagnosis, antimicrobial therapy)
o Collector’s name or initials
Types of Specimens
o Blood
o Urine
o Sputum
o Stool
o CSF
o Swabs (throat, wound, vaginal, urethral)
o Body fluids (pleural, peritoneal, synovial)
Tip: Always include relevant clinical history. It helps the lab prioritize testing and choose
appropriate culture media.
Lecture -6
1.2. Specimen Transport
Key Principles:
A. Transport Time
Deliver specimens to the lab within 2 hours.
For delays, use appropriate preservatives or transport media.
B. Temperature Considerations
Most specimens: room temperature or refrigerated (2–8°C).
CSF: kept at body temperature if for culture.
Avoid freezing unless advised.
C. Transport Media
Stuart's or Amies medium for swabs.
Cary-Blair for stool samples.
Viral Transport Medium (VTM) for viral samples.
Recommendation: Use leak-proof, sealed containers and follow UN3373 packaging standards
for biological substances during transport.
1.3. Specimen Processing
Key Principles:
Prompt Processing: Delay in processing reduces viability and may allow overgrowth
of commensal organisms.
Standard Operating Procedures (SOPs): Follow CDC or WHO protocols for:
o Culture
o Microscopy
o Molecular or serological testing
Use of Biosafety Cabinets (BSC): For aerosol-generating procedures and high-risk
pathogens.
1.4. Identification of Pathogenic Organisms:
A. Direct Examination
Microscopy: Gram stain, Ziehl-Neelsen stain, wet mounts.
Used for preliminary diagnosis (e.g., pus cells, bacteria, parasites).
B. Culture Methods
Agar media: Blood agar, MacConkey, Chocolate agar, Sabouraud agar.
Aerobic vs. anaerobic conditions.
Observe for colony morphology, hemolysis, pigmentation.
Lecture -6
C. Biochemical Identification
Tests: Catalase, coagulase, TSI, Indole, Citrate, Urease, API strips.
Used to confirm bacterial identity.
D. Serology
ELISA, latex agglutination, Widal test.
Helpful for detecting antibodies or antigens (e.g., HIV, Hepatitis B, Typhoid).
E. Molecular Methods
PCR, RT-PCR, GeneXpert.
Fast, sensitive, used for TB, COVID-19, STDs.
1.5. Quality and Safety Considerations
Follow Biosafety Level (BSL) procedures.
Dispose of waste according to biohazard protocols.
Maintain cold chain and logbooks.
Participate in External Quality Assessment (EQA) schemes.
2. The Role of Medical Professionals in Ensuring
Diagnostic Accuracy
Healthcare providers play a vital role in the diagnostic process, beginning with the decision
to order a test and ending with the interpretation of results.
2.1. Pre-Analytical Responsibilities
Selecting the Right Test and Specimen Type: Choose diagnostic tests that match
clinical symptoms and guide the lab on the correct specimen type.
Proper Specimen Collection: Ensure all team members are trained in standard
collection techniques.
Filling Out Request Forms Accurately: Provide detailed patient history, including:
o Travel history
o Exposure risks
o Immunization status
o Previous test results
Educating Patients: Especially important for self-collected specimens like sputum or
stool.
Lecture -6
2.2. Analytical Oversight (in collaboration with lab personnel)
Understand Diagnostic Tests: Know what a positive/negative result means, and its
sensitivity/specificity.
Ensure Timely Communication: Work with labs to prioritize urgent or critical
specimens.
2.3. Post-Analytical Responsibilities
Interpreting Results Appropriately: Consider clinical context, test limitations, and
patient immune status.
Communicating Results: Relay findings clearly to patients and document
appropriately.
Initiating Correct Treatment: Base therapy on confirmed lab results when
available.
CDC Guidance: Diagnostic stewardship is as important as antimicrobial stewardship — both
reduce resistance and improve patient outcomes.
Quote: “The laboratory result is only as good as the specimen collected.”
VI. Case Discussion and Q&A (Optional if time permits)
Case Example: A 30-year-old male presents with fever and productive cough. Sputum is
collected and processed for AFB and bacterial culture. Discuss collection, handling, and
interpretation of results.
