Sample collection and shipping
Specimen collection
May 2007
Laboratory Training for Field Epidemiologists
“Results are as good as specimen”
The procedures were developed to provide for the best
possible recovery of pathogenic microorganisms in samples
submitted for microbiological examination.
Medica Lab is NABL accredited
Learning objectives
At the end of the presentation, participants
should understand the:
• Procedures, preparation, processing and transport of
specimens
Medica Lab is NABL accredited
Successful laboratory
investigations
Advance planning
Collection of adequate and appropriate specimens
Sufficient documentation
Biosafety and decontamination
Correct packaging
Rapid transport
Medica Lab is NABL accredited
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 microbiologist, clinicians and
epidemiologist
Medica Lab is NABL accredited
Transport medium
Allows organisms (pathogens and contaminants)
to survive
Non-nutritive - does not allow organisms to
proliferate
For bacteria – i.e., Cary Blair
For viruses - virus transport media (VTM)
Medica Lab is NABL accredited
URINE
Medica Lab is NABL accredited
URINE
•The urine collected in a
wide mouthed container
from patients
•A mid stream specimen
is the most ideal for
processing
Medica Lab is NABL accredited
Specimens Types
Varies in method used and in time frame in which to collect
specimen
Types of specimens:
• Random
• First morning
• Clean catch midstream
• Timed
• 24 hour
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Methods of Urine Collection
Medica Lab is NABL accredited
collection process: Clean catch midstream
Take a pre-labelled Clean prepuce and glance/ labia with clean
sterile container water and clean your hands
Pass first third of the urine in
toilet, collect middle third
Open the container just before urinating
portion, again pass the final
third portion in toilet
Secure the container with lead Do not touch the container with any parts
after collection of the body, clothing or external surface
Send to lab as early as possible
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collection process: Catheter specimen
Medica Lab is NABL accredited
collection process: Catheter specimen
Medica Lab is NABL accredited
Medica Lab is NABL accredited
collection process: Supra pubic aspiration
• On rare occasions, the health
care provider may collect a urine
sample by inserting a needle
directly into the bladder
(suprapubic tap)
• This method is used when a
bedridden patient cannot be
catheterized or a least
contaminated specimen is
required or in case of infants.
• technically competent staffs are
required.
Medica Lab is NABL accredited
Caution – Never Collect Urine from Urine Bags for
Microbiological Testing
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SPUTUM
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Sputum sample collection
• Robust
• Leak-proof
• Sterile
• 50-ml capacity
• Translucent or clear material
• Single-use
• Wide-mouthed, screw-capped with
a watertight seal
• Easily-labelled walls
Medica Lab is NABL accredited
Sputum sample collection
• To be collected with out rinsing mouth or brushing
• Instruct patient to take a deep breath for 2-3 times
and cough out as hard as possible directly into a wide-
mouth sterile container
• Avoid mixing saliva or nasal secretion
• Minimum volume: 2 ml (optimal volume: 5 ml)
Medica Lab is NABL accredited
Medica Lab is NABL accredited
E.T. SUCTION
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E.T. suction collection process
Medica Lab is NABL accredited
E.T. suction collection process
• The patient should be hyper oxygenated by the delivery of
100% oxygen for >30 seconds prior to the suctioning
• Position the patient in supine position.
• Auscultate the breath sounds.
• Maintain appropriate pressure
adults-100-120 mmHg
children-50-100 mmHg
infants-40-60 mmHg
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E.T. suction collection process
• Wash hands
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E.T. suction collection process
• Wear sterile gloves and PPE, maintain sterile technique
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BLOOD
Medica Lab is NABL accredited
Medica Lab is NABL accredited
Blood culture: Procedure
• Hand hygiene.
• Position the patient.
• Bring all the equipment bedside or procedure bed.
• Tie tourniquet, select a vein and release the tourniquet.
• Clean the site with Chlorhexidine (2 to 2.5%) sol with circular
motion from centre to periphery.
• Allow the site to air dry.
• Do not touch the venipuncture site after it is cleaned.
• Remove over-caps from anaerobic and aerobic bottles and
clean the top of each bottle with a separate sterile alcohol
pad.
• wear a sterile gloves.
Medica Lab is NABL accredited
Blood culture: Procedure
• Collect appropriate volume of blood
• Change the needle with fresh sterile one then inject the
required blood in each culture bottle.
• Do not allow air to enter bottle. Invert to mix.
• Do not allow the blood to clot before or after being added to
the culture bottle.
Medica Lab is NABL accredited
Blood culture: Procedure
Venous blood
• infants: 0.5 – 2 ml
• children: 2 – 5 ml
• adults: 5 – 10 ml
• 2 -3 sets
• Different sites
• From device
Medica Lab is NABL accredited
Medica Lab is NABL accredited
Cerebrospinal fluid (CSF)
Collection
Lumbar puncture
Sterile tubes
Aseptic conditions
Trained person
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CSF
Handling and transportation
Bacteria
• preferably in trans-isolate medium, pre-
warmed to 25-37°C before inoculation
OR
• transport at ambient temperature (relevant pathogens do not
survive at low temperatures)
Viruses
• transport at 4-8oC (if up to 48hrs or -70oC for longer duration)
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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
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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
Medica Lab is NABL accredited
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
WHO/CDS/EPR/ARO/2006.1
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Biosafety: protect the patient
Use single use equipment
Disinfect
Work in a clean, dedicated area
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Biosafety: protect yourself
Use personal protective equipment
–disposable gloves
–laboratory coats / gown
–mask
–protective eyewear / face shields if procedure is likely
to generate aerosols
If no sharps container: collect sharps immediately to prevent needle-
stick injury
Have first aid kit readily accessible
Do not reuse contaminated equipment
Medica Lab is NABL accredited
Biosafety: protect others, the environment
Package samples appropriately for transport
Decontaminate spills - 10% bleach after wiping the surface clean
Disinfect working areas for future use - 1% household bleach daily
Soak contaminated non-disposable equipment/material in 1%
household bleach for 5 minutes
– wash in soapy water before re-use, sterilize if necessary
Place waste in leak-proof biohazard bags - ensure safe final
management of waste
Protect cleaning/decontamination personnel with protective coat, thick
rubber gloves
Medica Lab is NABL accredited
Infection control precautions
Precautions Use Requirements
Contact Patients known or suspected to have •Gloves
precautions serious illnesses easily transmitted •Gown
by direct patient contact or by
contact with items in the patient's
environment
Droplet Barrier to stop infections spread by •Contact precautions
precautions large (>5 microns), moist droplets •Well-fitting mask
produced by people when they •Eye protection
cough, sneeze or speak
Airborne Patients known or suspected to have •Contact precautions
precautions serious illnesses transmitted by •Droplet precautions
airborne droplet nuclei • N95 mask
•Isolation room
(In hospital)
Medica Lab is NABL accredited
Criteria for rejecting samples
Mismatch of information on the label and the request
Inappropriate transport temperature
Excessive delay in transportation
Inappropriate transport medium
– specimen received in a fixative
– dry specimen
– sample with questionable relevance
Insufficient quantity
Leakage
Medica Lab is NABL accredited
