Pathology Specimens: Types, Collection Principles, Containers, Tests and Interpretation

Learning objectives

• Classify pathology specimens as blood, fluid, tissue, cytology, microbiology, molecular and point-of-care samples.
• Select an appropriate specimen for common haematology, chemistry, microbiology, histology, cytology and molecular tests.
• Explain whole blood, serum, plasma, anticoagulant tubes and blood-culture specimens.
• Describe urine, stool, sputum, swab, CSF, serous-fluid, synovial-fluid, tissue and bone-marrow specimens.
• Apply patient identification, consent, labelling, biosafety, adequacy and rejection principles before sending a sample.
• Recognise common pre-analytical errors and communicate clinically important information to the laboratory.

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1. What makes a specimen diagnostically useful?

Requirement	Question before collection	Common failure
Right patient	Have identity and identifiers been confirmed using the local policy?	Wrong-patient result or unlabeled sample.
Right test	What clinical question will the result answer?	“Routine bloods” with no diagnosis or timing.
Right site	Is the sample from the active lesion or sterile compartment?	Superficial swab instead of deep tissue or aspirate.
Right timing	Before antibiotics? During fever? Fasting? Peak/trough drug level?	False-negative culture or uninterpretable hormone/drug level.
Right container	Which anticoagulant, fixative, transport medium or sterile container is required?	EDTA sent for chemistry, formalin sent for culture, clotted blood for CBC.
Enough volume	Is there enough material for all requested tests and repeat/confirmatory work?	Insufficient CSF or blood-culture volume.
Safe handling	Can the specimen be collected without aerosol, sharps or splash exposure?	Leaking container, unsafe recapping or unsealed swab.
Clinical information	What symptoms, suspected disease, treatment and exposure matter?	Laboratory cannot interpret an unusual specimen or prioritise urgent work.

2. Major specimen categories

Category	Examples	Main laboratory disciplines
Blood	Whole blood, serum, plasma, blood culture, peripheral smear, arterial/venous blood gas.	Haematology, chemistry, immunology, microbiology, transfusion, molecular testing.
Urine	Random, first-morning, clean-catch midstream, catheter, timed, 24-hour, urine culture.	Urinalysis, microscopy, chemistry, microbiology, toxicology, pregnancy and molecular testing.
Stool	Fresh faeces, rectal swab, ova-and-parasite sample, occult-blood sample.	Parasitology, microbiology, chemistry, inflammatory markers and molecular tests.
Respiratory	Sputum, induced sputum, nasopharyngeal/throat swab, bronchoalveolar lavage, tracheal aspirate.	Microbiology, TB testing, cytology and molecular respiratory panels.
Body fluids	CSF, pleural, ascitic, pericardial, synovial, amniotic and dialysate fluids.	Cell count, chemistry, microbiology, cytology and crystal analysis.
Tissue	Biopsy, excision, curettage, placenta, surgical specimen and autopsy tissue.	Histopathology, special stains, immunohistochemistry and molecular pathology.
Cytology	Fine-needle aspirate, exfoliative cells, cervical smear, effusion and brushings.	Cell morphology, cytochemistry, immunocytochemistry and molecular tests.
Other	Skin, hair, nails, genital specimens, semen, ocular fluid, ear swab and wound aspirate.	Microbiology, mycology, parasitology, cytology, chemistry and fertility testing.

3. Blood specimens

3.1 Whole blood

Whole blood contains cells suspended in plasma. It is used when the cellular component or blood-cell–plasma relationship must be preserved.

Specimen	Common tests	Container/important principle
EDTA whole blood	Full blood count, blood film, reticulocytes, HbA1c and some molecular tests.	Lavender/purple-top EDTA tube; fill adequately and mix gently. Clots invalidate cell counts.
Citrate whole blood/plasma	PT/INR, aPTT, fibrinogen and selected coagulation tests.	Light-blue citrate tube; correct blood-to-citrate ratio is essential. Underfilling falsely prolongs results.
Heparinised blood	Some chemistry tests, blood gases and point-of-care analysis.	Green-top heparin tube or balanced heparin blood-gas syringe; avoid air bubbles for blood gases.
Fluoride/oxalate blood	Selected glucose/lactate testing where local protocol specifies.	Grey-top tube; additive inhibits glycolysis but is not interchangeable with every glucose method.
Blood-gas specimen	pH, PaO₂, PaCO₂, bicarbonate, lactate.	Arterial, venous or capillary blood in heparinised syringe; remove air and send promptly.
Peripheral blood film	Malaria parasites, abnormal cells, haemolysis, blasts and red-cell morphology.	Fresh EDTA blood or correctly prepared smear; state travel, fever and suspected malaria.

3.2 Serum

Serum is the liquid remaining after blood clots and is centrifuged. It lacks fibrinogen and many clotting factors. It is used for chemistry, serology, hormones, therapeutic drug monitoring and many immunology tests.

• Allow clotting according to local laboratory instructions before centrifugation.
• Haemolysis, lipaemia and icterus can interfere with photometric and biochemical tests.
• Do not send serum in an EDTA tube or contaminate it with anticoagulant from another tube.

3.3 Plasma

Plasma is obtained by centrifuging anticoagulated blood and retains fibrinogen. It may be lithium-heparin plasma for chemistry, citrate plasma for coagulation or EDTA plasma for selected assays.

Order of draw: follow the local laboratory order-of-draw policy to reduce additive carryover. Never rely on memory when multiple tube types are collected.

3.4 Blood cultures

Blood cultures detect viable organisms in blood and are most useful when collected before antimicrobial therapy and during suspected bloodstream infection. Collect the number and volume of sets specified by local policy, using strict skin antisepsis and separate venepuncture sites when possible.

• Document fever, chills, suspected source, antibiotic timing and collection site.
• Do not draw through an IV line unless line infection is specifically being assessed and the source is labelled.
• Insufficient volume is a major cause of false-negative cultures; contamination causes unnecessary antibiotics and prolonged admission.
• Alert the laboratory about suspected high-consequence pathogens and follow biosafety instructions.

4. Urine specimens

Type	Best use	Collection principles
Random urine	Routine urinalysis, dipstick and microscopy.	Clean, labelled container; record time and hydration context.
First-morning urine	Concentrated sediment, pregnancy testing, albumin or selected molecular tests.	Collect on waking before excessive fluid intake.
Clean-catch midstream	Urine culture and sensitivity.	Clean external genital area, begin voiding, collect midstream without touching inside of container.
Catheter urine	When a catheterised patient cannot provide a clean sample or line infection is assessed.	Collect from the sampling port, never from the drainage bag.
Timed/24-hour urine	Creatinine clearance, protein, electrolytes, hormones and selected metabolites.	Discard the first void, record start time, collect all urine, include final void at end time.
Suprapubic aspirate	Selected infants or complicated cases when contamination must be minimised.	Invasive procedure by trained staff; use sterile technique.

Contamination from skin, vaginal secretions, poor storage or collection from a bag can mimic urinary infection. Interpret urinalysis, symptoms, culture and antibiotic exposure together.

5. Stool and rectal specimens

• Fresh stool: used for microscopy, culture, antigen, toxin, inflammatory markers and molecular tests.
• Ova-and-parasite specimen: timing and number of samples depend on suspected parasite and local protocol; state travel, eosinophilia and immunosuppression.
• Rectal swab: useful when stool cannot be obtained or for selected outbreak/sexual-health testing; it is not a universal replacement for stool.
• Occult-blood sample: use the kit and dietary/medicine instructions of the specific test.
• Stool culture: collect before antibiotics when possible and provide history of diarrhoea, travel, outbreak, food exposure and immunocompromise.

Do not contaminate stool with urine, water, disinfectant or toilet paper. Bloody, mucoid or watery portions may be diagnostically more useful for some tests.

6. Respiratory specimens

6.1 Sputum

Sputum is lower-respiratory secretion produced by coughing, not saliva. It is used for bacterial culture, TB smear/NAAT/culture, cytology and selected fungal studies.

• Collect after mouth rinsing with clean water; avoid toothpaste or antiseptic mouthwash immediately before collection when local protocol advises.
• Use a sterile, leak-proof, wide-mouth container.
• Teach deep cough from the chest; saliva-only specimens may be rejected as poor quality.
• Collect before antibiotics if clinically safe; state TB risk, haemoptysis and immune status.

6.2 Swabs and aspirates

Nasopharyngeal, nasal, throat, conjunctival, wound and genital swabs require the correct flocked swab and transport medium for the test. A superficial wound swab may reflect colonisation; aspirate or deep tissue is often more representative.

6.3 Bronchoalveolar lavage and tracheal aspirate

These are collected by trained teams in selected respiratory disease. Label the anatomical site, laterality and procedure. Interpret results with clinical and radiographic findings because colonisation is common in intubated patients.

7. Cerebrospinal fluid (CSF)

CSF is usually collected by lumbar puncture into sequential sterile tubes. It is a precious, time-critical specimen for meningitis, encephalitis, subarachnoid haemorrhage, inflammatory disease and malignancy.

CSF investigation	What it answers	Important information
Opening pressure	Evidence of raised or low intracranial pressure.	Record patient position and technique.
Cell count/differential	Inflammatory, infectious or malignant cellular response.	Send promptly; traumatic tap changes interpretation.
Protein/glucose	Blood–CSF barrier and metabolic/infectious pattern.	Send paired blood glucose when interpreting CSF glucose.
Gram stain/culture	Bacterial infection and antimicrobial susceptibility.	Collect before antibiotics when possible, but do not delay treatment in a critically ill patient.
NAAT/PCR	Viral, bacterial, TB or other pathogen DNA/RNA.	Use the correct volume and tube; specify suspected pathogen.
Cytology/flow cytometry	Malignant cells or abnormal lymphoid populations.	Large enough volume and prompt processing improve yield.

8. Serous and other body fluids

Fluid	Common diagnostic questions	Typical tests/specimen needs
Pleural fluid	Transudate or exudate? Infection, malignancy, TB, haemorrhage or chyle?	Cell count, protein/LDH paired with serum, glucose, pH in blood-gas syringe, Gram/culture, cytology and selected TB tests.
Ascitic fluid	Portal hypertension, bacterial peritonitis, malignancy, pancreatic or chylous ascites?	Cell count/differential, albumin/protein, culture inoculated into blood-culture bottles when indicated, cytology and selected tests.
Pericardial fluid	Infection, malignancy, autoimmune, haemorrhage or chylous process?	Cell count, chemistry, culture, cytology and molecular tests as clinically indicated.
Synovial fluid	Septic arthritis, crystal arthritis, inflammatory or non-inflammatory disease?	Appearance, viscosity, cell count, Gram/culture and crystal analysis by polarised microscopy.
Amniotic fluid	Fetal, infection, maturity or genetic questions in specialist care.	Strict consent, labelling and specialist protocol.
Dialysate	Peritonitis or treatment adequacy.	Cell count, differential, culture and chemistry using the local renal protocol.

Fluid specimens should be labelled with exact anatomical site, side, procedure and clinical suspicion. A “body fluid” label without site is unsafe because normal values and organisms differ by compartment.

9. Tissue specimens for histopathology

9.1 Biopsy types

• Incisional biopsy: a representative part of a lesion is sampled.
• Excisional biopsy: the entire small lesion is removed, often for diagnosis and treatment.
• Core/needle biopsy: a cylindrical tissue sample obtained percutaneously or endoscopically.
• Endoscopic biopsy: mucosal tissue taken during endoscopy.
• Curettage: tissue scraped from a cavity or lining.
• Bone marrow trephine/aspirate: evaluates haematological, infiltrative and metastatic disease.
• Placenta and products of conception: submitted when clinical indications, recurrent loss, infection or abnormality warrant examination.

9.2 Tissue handling choices

Destination	Specimen state	Reason
Routine histology	Fresh tissue placed promptly in appropriate fixative, commonly buffered formalin according to laboratory volume ratio.	Preserves architecture for microscopy.
Microbiology	Sterile fresh tissue or aspirate in a sterile container; no formalin.	Fixative kills organisms and prevents culture.
Frozen section	Fresh, unfixed tissue sent immediately with the question and contact details.	Rapid intraoperative assessment.
Immunohistochemistry	Well-fixed paraffin tissue or validated fresh/frozen material.	Detects proteins and cell lineage.
Molecular pathology	Validated fixed tissue, fresh tissue, blood, marrow or swab depending on assay.	Detects mutations, fusions, pathogens or clonality.
Electron microscopy	Very small piece placed in specialised fixative.	Preserves ultrastructure in selected diseases.

10. Cytology specimens

Cytology examines individual cells rather than tissue architecture.

• Exfoliative cytology: cells shed into sputum, urine, effusions or cervical samples.
• Fine-needle aspiration: cells aspirated from a thyroid, lymph node, breast, salivary gland or mass.
• Brushings/washings: cells collected from respiratory, gastrointestinal or urinary epithelium.
• Liquid-based cytology: cells suspended in preservative for preparation and ancillary testing.

Record site, laterality, lesion size, imaging findings, previous cancer, treatment and whether cell-block, flow cytometry or molecular testing is required. A cytology diagnosis may be limited when architecture or invasion cannot be assessed.

11. Bone marrow and haematology specimens

• Bone-marrow aspirate: cellular morphology, differential count, iron, flow cytometry, cytogenetics and molecular testing.
• Trephine biopsy: marrow architecture, cellularity, fibrosis, infiltrative disease and focal lesions.
• Peripheral blood: CBC, film, malaria parasites, haemolysis and selected molecular assays.
• Transfusion specimens: correctly labelled EDTA blood for group, screen, cross-match and antibody investigation; bedside identity checks are critical.

Coordinate marrow collection with the laboratory so that fresh material reaches the correct sections before it clots or dries.

12. Skin, hair, nails and ocular/genital specimens

Specimen	Common use	Collection principle
Skin scraping	Fungal microscopy/culture, scabies or selected parasitology.	Sample active edge or burrow as directed; avoid topical treatment immediately before collection when possible.
Hair/nail clipping	Dermatophyte testing, toxicology or mineral analysis.	Clean site and collect affected material in a dry sterile container.
Wound aspirate/tissue	Deep infection and susceptibility testing.	Clean surface first; aspirate pus or submit tissue rather than a superficial swab when feasible.
Conjunctival/ocular fluid	Ocular infection or inflammation.	Use the correct swab or sterile fluid container; ophthalmology guidance may be required.
Genital/cervical swab	STI NAAT, culture, microscopy or cytology.	Correct site, patient consent, pregnancy status and test-specific transport medium.
Semen	Fertility, infection or post-vasectomy analysis.	Follow abstinence, collection, timing and transport instructions exactly.

13. Specimens by laboratory discipline

Discipline	Specimens	Questions answered
Haematology	EDTA blood, citrate plasma, marrow.	Cell numbers/morphology, coagulation, anaemia, leukaemia and bleeding risk.
Clinical chemistry	Serum, plasma, urine, CSF and body fluids.	Electrolytes, organ function, glucose, enzymes, hormones and metabolites.
Microbiology	Blood, urine, stool, sputum, swabs, tissue, CSF and fluids.	Organism detection, identification, susceptibility and infection control.
Histopathology	Biopsy, excision, curettage, placenta and autopsy tissue.	Architecture, injury, inflammation, tumour type, grade and margins.
Cytology	FNA, effusions, urine, sputum, brushings and cervical samples.	Cell morphology, malignancy and selected ancillary markers.
Immunology/serology	Serum, plasma, CSF and occasionally tissue.	Antibodies, antigens, autoimmunity, allergy and immune status.
Molecular diagnostics	Blood, swab, tissue, CSF, urine, marrow and extracted nucleic acid.	Pathogen DNA/RNA, mutations, fusions, clonality and inherited variants.

14. Patient preparation and collection safety

• Explain the procedure, purpose, discomfort, risks and expected timing; obtain consent where required.
• Check fasting, posture, exercise, medication timing, menstrual cycle, pregnancy and recent transfusion when relevant.
• Use standard precautions for every specimen; add transmission-based precautions for suspected high-risk infection.
• Use gloves, eye/face protection and sharps safety according to risk. Never recap needles.
• Clean the correct site with the approved antiseptic and allow it to dry.
• Use leak-proof, labelled containers and place them in a biohazard bag with the request form kept separate from the specimen compartment.
• Tell the laboratory about suspected TB, viral haemorrhagic fever, prion disease or other high-consequence infection before sending.

15. Labelling and request-form essentials

Item	What to include
Patient identifiers	Full name plus approved second identifier (date of birth, hospital number or national identifier).
Specimen details	Type, exact anatomical site, side, collection date/time and collector identity.
Clinical information	Symptoms, working diagnosis, exposure, pregnancy, immune status, antibiotics and relevant history.
Tests requested	Specific tests and urgency; avoid vague “screening” without a clinical question.
Safety information	Suspected high-risk pathogen, isolation status and contact number for urgent results.
Consent/procedure	Document consent and procedure details for invasive collections and tissue.

16. Specimen adequacy and rejection

Laboratories reject specimens when the risk of an incorrect result outweighs the benefit of testing. Rejection criteria should be written in local SOPs, but common reasons include:

• Unlabelled, mismatched or incompletely identified container.
• Wrong container, wrong preservative or expired transport medium.
• Insufficient quantity, dried swab or specimen leaked/contaminated externally.
• Clotted blood for a test requiring anticoagulated blood.
• Severe haemolysis, lipaemia or sample dilution that invalidates the requested assay.
• Specimen from the wrong site or superficial material that does not answer the question.
• Excessive delay or temperature exposure that alters cells, organisms or analytes.
• Form missing clinical information or high-risk alert.

When rejection could harm the patient, the laboratory should contact the clinical team, document the reason and help arrange safe recollection. Never silently process an unsafe or unidentifiable specimen.

17. Choosing a specimen: clinical examples

Clinical question	Preferred specimen	Common wrong specimen
Suspected bacterial meningitis	CSF plus blood cultures, collected safely and urgently.	Only a throat swab or delayed CSF after antibiotics without documentation.
Suspected urinary infection	Clean-catch midstream urine or appropriate catheter-port specimen.	Urine from the drainage bag.
Deep wound infection	Aspirate or tissue after cleaning.	Surface swab of colonised skin.
Pulmonary TB	Quality sputum or induced sputum for smear/NAAT/culture per protocol.	Saliva or a dry swab.
Sepsis	Appropriate blood-culture sets plus source-specific specimens before antibiotics when feasible.	One underfilled bottle after antibiotics only.
Acute leukaemia	EDTA blood, marrow aspirate/trephine and fresh material for flow/cytogenetics.	Formalin-only marrow when flow cytometry is needed.
Ascites with fever	Fresh ascitic fluid for cell count and culture, with additional chemistry/cytology as indicated.	Only a serum sample or unlabelled “fluid.”
Suspected malignancy	Representative tissue or cytology with site, imaging and clinical history.	Crushed, cauterised or poorly oriented tissue without site information.

18. Pre-analytical errors and clinical consequences

• Wrong patient: leads to incorrect treatment, transfusion or disclosure of another person’s result.
• Wrong site: can miss infection, tumour margins or focal disease.
• Wrong timing: may miss bacteraemia, alter hormone/drug levels or produce a false-negative culture.
• Wrong container: additives cause dilution, clotting or assay interference.
• Haemolysis: releases intracellular analytes and may falsely raise potassium, LDH and AST.
• Contamination: produces false-positive cultures, unnecessary antibiotics and prolonged admission.
• Insufficient volume: reduces sensitivity, especially in blood cultures and low-volume CSF.
• Delayed processing: changes cell morphology, glucose, gases, organism survival and nucleic-acid quality.

19. Clinical cases

20. High-yield revision table

Specimen	Remember
EDTA blood	CBC/film/HbA1c; clots are unacceptable.
Citrate blood	Coagulation; correct fill ratio matters.
Serum	Clot first; chemistry, hormones and serology.
Heparin blood	Some chemistry and blood gases; follow local policy.
Blood culture	Before antibiotics if feasible; adequate volume and asepsis.
Clean-catch urine	Midstream, not bag urine; prevent contamination.
Sputum	Deep lower-respiratory secretion, not saliva.
CSF	Time-critical; label tubes and tests; never delay lifesaving treatment.
Body fluid	State exact site and side; send tests matched to the question.
Tissue	Fixative for histology; fresh sterile tissue for culture/flow/molecular tests.
Cytology	Cells rather than architecture; specify site and ancillary tests.

21. Quick self-test

1. What is the difference between whole blood, plasma and serum?
2. Why should urine culture not be collected from a catheter drainage bag?
3. How can a clinician divide a mass specimen for histology and microbiology?
4. Why can a superficial wound swab mislead treatment?
5. List the identifiers that must appear on a specimen and request form.
6. What makes CSF a time-critical specimen?
7. Give three reasons a laboratory may reject a sample.

22. Key take-home points

• The specimen is the foundation of laboratory quality; a perfect assay cannot rescue a wrong or poor sample.
• Choose the sample that best represents the disease site and clinical question.
• Blood type, anticoagulant, volume, timing and mixing determine what can be measured.
• Urine, sputum, stool and swabs are easily contaminated; teach collection carefully.
• CSF, blood cultures, sterile fluids and tissue for suspected high-risk infection require urgent, safe handling.
• Formalin preserves tissue architecture but is unsuitable for culture and some fresh-cell tests.
• Label the exact anatomical site, side, date/time and patient identifiers.
• Include suspected diagnosis, antibiotics, immune status, pregnancy and high-risk exposures.
• Do not silently accept an unidentifiable or unsafe specimen; recollect safely and document the reason.
• The next post will address Specimen Preservation, followed by Specimen Transportation.

Sources and further reading

• WHO Laboratory Biosafety Manual, 4th edition
• WHO Laboratory Quality Management System handbook
• WHO sample collection kit: blood, CSF, stool, urine, skin and respiratory samples
• WHO LQSI sample acceptance and rejection criteria
• WHO LQMS sample collection, preservation and transport resource
• CDC infection-control and chain-of-infection principles
• NCBI/IARC biological specimen collection and biobank standards