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Laboratory specimen: collection, safe transport and biosafety


Specimen Collection Laboratory specimen: collection, safe transport and biosafety * Slide * Sputum This indicates how to collect sputum. – PowerPoint PPT presentation

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Title: Laboratory specimen: collection, safe transport and biosafety

Laboratory specimen collection, safe transport
and biosafety
Specimen Collection
Learning objectives
  • At the end of the presentation participants
    should be able to
  • Explain the procedures, preparation, processing
    and transport of specimens

Successful laboratory investigations
  • advance planning
  • collection of appropriate and adequate specimens
  • labeling and documentation of laboratory specimen
  • storage, packaging and transport to appropriate
  • the ability of the laboratory to accurately
    perform the diagnostic tests
  • biosafety and decontamination procedures to
    reduce the risk of further spread of the disease
  • timely communication of results

Specimen collection key issues
  • Consider differential diagnoses
  • Decide on test(s) to be conducted
  • Decide on clinical samples to be
  • collected to conduct these tests
  • consultation between microbiologists, clinicians
    and epidemiologists

Transport medium
  • Allows organisms (pathogens and contaminants) to
  • Non-nutritive - does not allow organisms to
  • For bacteria i.e., Cary Blair
  • For viruses - virus transport media (VTM)

Some tips
  • Laboratory investigation should start as early as
  • Specimens obtained early, preferably prior to
    antimicrobial treatment likely to yield the
    infective pathogen
  • Before doing anything, explain the procedure to
    patient and relatives
  • When collecting the specimen, avoid contamination
  • Take a sufficient quantity of material
  • Follow the appropriate precautions for safety

Blood for smears
  • Collection
  • Capillary blood from finger prick
  • make smear
  • fix with methanol or other fixative
  • Handling and transport
  • Transport slides within 24 hours
  • Do not refrigerate (can alter cell morphology)

Blood for cultures
  • Collection
  • Venous blood
  • infants 0.5 2 ml
  • children 2 5 ml
  • adults 5 10 ml
  • Requires aseptic technique
  • Collect within 10 minutes of fever
  • if suspect bacterial endocarditis 3 sets of
    blood culture

Blood for cultures
  • Handling and Transport
  • Collect into bottles with infusion broth
  • change needle to inoculate the broth
  • Transport upright with cushion
  • prevents hemolysis
  • Wrap tubes with absorbent cotton
  • Travel at ambient temperature
  • Store at 4oC if cant reach laboratory in 24

  • Collection
  • Venous blood in sterile tube
  • let clot for 30 minutes at ambient temperature
  • glass better than plastic
  • Handling
  • Place at 4-8C for clot retraction for at least
    1-2 hours
  • Centrifuge at 1 500 RPM for 5-10 min
  • separates serum from the clot

  • Transport
  • 4-8oC if transport lasts less than 10 days
  • Freeze at -20C if storage for weeks or months
    before processing and shipment to reference
  • Avoid repeated freeze-thaw cycles
  • destroys IgM
  • To avoid hemolysis do not freeze unseparated

Cerebrospinal fluid (CSF)
  • Collection
  • Lumbar puncture
  • Sterile tubes
  • Aseptic conditions
  • Trained person

  • Handling and transportation
  • Bacteria
  • preferably in trans-isolate
    pre-warmed to 25-37C
    before inoculation
  • OR
  • transport at ambient temperature (relevant
    pathogens do not survive at low temperatures)
  • Viruses
  • transport at 4-8C (if up to 48hrs or -70C for
    longer duration)

Rectal swabs
  • Advantage
  • convenient
  • adapted to small children, debilitated patients
    and other situations where voided stool sample
    not feasible
  • Drawbacks
  • no macroscopic assessment possible
  • less material available
  • not recommended for viruses

Stool samples
  • Collection
  • Freshly passed stool samples
  • avoid specimens from a bed pan
  • Use sterile or clean container
  • do not clean with disinfectant
  • During an outbreak - collect from 10-20 patients

Stool samples for viruses
  • Timing
  • within 48 hours of onset
  • Sample amount
  • 5-10 ml fresh stool from patients (and controls)
  • Methods
  • fresh stool unmixed with urine in clean, dry and
    sterile container
  • Storage
  • refrigerate at 4C do not freeze
  • store at -15C - for Ag detection, polymerase
    chain reaction (PCR)
  • Transport
  • 4C (do not freeze) dry ice for (Ag detection
    and PCR)

Stool samples for bacteria
  • Timing
  • during active phase
  • Sample amount and size
  • fresh sample and two swabs from patients,
    controls and carriers (if
  • Method
  • Cary-Blair medium
  • For Ag detection/PCR no transport medium
  • Storage
  • refrigerate at 4C if testing within 48 hours,
    -70C if longer store at -15C for Ag detection
    and PCR
  • Transport
  • 4C (do not freeze) dry ice for Ag, PCR

Stool samples for parasites
  • Timing
  • as soon as possible after onset
  • Sample amount and size
  • at least 3 x 5-10 ml fresh stool from patients
    and controls
  • Method
  • mix with 10 formalin or polyvinyl chloride, 3
    parts stool to 1 part preservative
  • unpreserved samples for Ag detection and PCR
  • Storage
  • refrigerate at 4C store at -15C for Ag
    detection and PCR
  • Transport
  • 4C (do not freeze) dry ice for antigen
    detection and PCR

Throat swab (posterior pharyngeal swab)
  • Hold tongue away with tongue depressor
  • Locate areas of inflammation and exudate in
    posterior pharynx, tonsillar region of throat
    behind uvula
  • Avoid swabbing soft palate do not touch tongue
  • Rub area back and forth with cotton or Dacron swab

Nasopharyngeal swab
  • Tilt head backwards
  • Insert flexible fine-shafted polyester swab into
    nostril and back to nasopharynx
  • Leave in place a few seconds
  • Withdraw slowly rotating motion

Nasopharyngeal aspirate
  • Tilt head slightly backward
  • Instill 1-1.5 ml of VTM /sterile normal saline
    into one nostril
  • Use aspiration mucus trap
  • Insert silicon catheter in nostril and aspirate
    the secretion gently by suction in each nostril

  • Collection
  • Instruct patient to take a deep breath and cough
    up sputum directly into a wide-mouth sterile
  • avoid saliva or postnasal discharge
  • 1 ml minimum volume

Respiratory samples
  • Handling and Transport
  • All respiratory specimens except sputum are
    transported in appropriate media
  • bacteria Amies or Stuarts transport medium
  • viruses viral transport medium (VTM)
  • Transport as quickly as possible to the
    laboratory to reduce overgrowth by oral flora
  • For transit periods up to 24 hours
  • ambient temperature for bacteria
  • 4-8C for viruses

Post-mortem samples
  • Collection
  • Biopsy relevant tissues
  • place in formalin for histopathology
  • place in transport medium for microbiological
  • place in sterile saline for isolation of viral

Post-mortem samples
  • Handling and transportation
  • Fixed specimens can be transported at ambient
  • transport specimens in transport media within 24h
    at ambient temperature
  • transport specimens in sterile saline at 4-8oC
    within 48h

Virologic Investigations
Bacteriologic Investigations
Water for bacteriology
  • Preparation
  • Chlorinated water - add sodium thiosulphate
    (0.5ml of 10 solution or a small crystal)
  • Tap/ pump
  • remove attachments
  • wipe, clean and flame outlet
  • allow to flow (at least one minute)
  • Water course or reservoir - collect from a
    depth of at least 20 cm
  • Dug well - do not allow the bottle to touch the
    sides of the well

Water for bacteriology
  • Collection
  • At least 200 ml of water sample from the
  • In sterile glass bottles OR autoclavable plastic
  • tight screw capped lid
  • securely fitting stoppers/caps
  • an overhanging rim

Water for bacteriology
  • Handling and transportation
  • Test the water sample within 3 hours of
  • keep at ambient temperature
  • If delayed
  • pack sample on ice
  • test refrigerated sample within 24 hours

Food samples
  • Collect suspect food earliest
  • Collect aseptically - sterile tools, containers
  • Solid Food
  • cut 100-200 grams from centre with sterile knife
  • raw meat or poultry - refrigerate in a sterile
    plastic jar
  • Liquids
  • shake to mix, use sterile tube
  • water used for cooking -- 1-5 liters
  • Contact surfaces (utensils and/or equipment) for
    food processing
  • moisten swab with sterile 0.1 peptone water or
    buffered distilled water put the swab in an
    enrichment broth

Food samples
  • Handling and transportation
  • As fast as possible
  • Keep perishable food at 2-8 C
  • Cool hot food rapidly - put containers under cold
    running water
  • Pack samples to prevent spillage
  • Contact the laboratory regarding method of
    transport and anticipated time of receipt
  • Seek help from environmental/veterinary

Labeling specimens
  • Patients name (or Patient Identifier)
  • Unique ID number (Research/Outbreak)
  • Specimen type
  • Date, time and place of collection
  • Name/ initials of collector

Patients Name/Identifier Unique ID
Number RRR-0023 001712643003 Date,
Time, Place of Collection Sept 22, 2006, 1515 hr,
Maka Community Hospital, Barton, Capiz,
Philippines Specimen Type Serum Collected by MDR
Glass slides for microscopy
  • Label slides individually
  • use glass marking pencil
  • ensure markings dont interfere with staining
  • Each slide should bear
  • patient name
  • unique identification number
  • date of collection

Some Tips
  • Pre-print labels
  • Permanently affix label to the specimen
  • Glass slides for microscopy labeled individually
  • One specimen one lab request
  • Each slide should bear the patients name, unique
    identifier, and date of collection
  • Use line listing for multiple patients
  • Original documents kept by investigation team

Case investigation form
  • Epidemiologist sends
  • Patient information
  • age (or date of birth), sex, complete address
  • Clinical information
  • date of onset of symptoms, clinical and
    immunization history, risk factors or contact
    history where relevant, anti-microbial drugs
    taken prior to specimen collection
  • Laboratory information
  • acute or convalescent specimen
  • other specimens from the same patient
  • Line listing if large number of patients

Case investigation form
  • Receiving laboratory records
  • Date and time when specimen was received
  • Name and initials of the person receiving
  • Record of specimen quality


Criteria for rejecting samples
  • Mismatch of information on the label and the
  • Inappropriate transport temperature
  • Excessive delay in transportation
  • Inappropriate transport medium
  • specimen received in a fixative
  • dry specimen
  • sample with questionable relevance
  • Insufficient quantity
  • Leakage

  • Communicable Disease Toolkit Iraq Crisis.
    Guidelines for the collection of specimens for
    laboratory testing. WHO, 2003
  • Guidelines for the collection of clinical
    specimens during field investigation of
    outbreaks, WHO, 2000
  • The role of laboratories and blood banks in
    disaster situations, WHO publication, 2001
  • Sampling during avian influenza investigations,
  • IDSR guidelines for specimen collection, 2003
  • Laboratory Needs for Emergency Situations, 2003
  • Overview of Laboratory Structure and Operational
    Needs for the Iraqi Crisis, 2003
  • Costing for sampling materials and diagnostic
    reagents for the Iraq crisis, 2003

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