1. COLLECTION AND TRANSPORT
OF SPECIMENS

2. INTORDUCTION:
Specimen collection and transportation
are critical considerations , because any
results the laboratory generates is limited
by the quality of the specimen and its
condition on arrival in the laboratory.
Specimens should be obtained to minimize
the possibility of introducing contaminating
microorganisms that are not involved in
the infectious process.

3. General guidelines for
specimen collection:
⚫Depending on the type of infection
e.g. blood
⚫Aseptic precautions
⚫Anatomic sites and locations
⚫Adequate amount/volume
⚫Tissue or other body fluids should be
preferred over swabs, to get quality
material
⚫Proper timing
⚫Clinical laboratory form

4. An Ideal Request form
 Name xxxx
 IP/ OP No xyz
Age
Time
Sex
Date
 Ward xx123 Urgent / Routine
 Nature of specimen
 Investigation needed
Doctor/Staff
Contact No
1234567

5. ⚫Use of transport media
⚫Proper handling ,labelling and
transportation
⚫Use of proper container
⚫Instruction to the patient
⚫Before the administration of antibiotics
⚫Avoid contamination of specimens

6. SPECIMEN TRANSPORT:
⚫Within 2 hours of collection
⚫Containers should be leak-proof
⚫Separate section for paperwork
⚫Special preservatives or holding media
⚫Biohazard label

7. ⚫Triple packaging system

8. Criteria for rejection of
specimens:
Several criteria can be considered by a laboratory on the
basis of which the processing of a specimen may not be
done by the laboratory. Such a decision must be made in
light of the specific requested investigation. Laboratory
investigations of a sample are a waste of time and
resources if following criteria are not fulfilled :
⚫
⚫
⚫ Missing or inadequate identification
⚫ Insufficient quantity
⚫ Specimen collected in an inappropriate container
Contamination suspected Inappropriate
transport or storage

9. Containers and swab for
the collection of
specimens:
Containers:
For faeces:-
• Universal container
•Spoon attached to the
inside of the screw cap

10. For urine:-
⚫ Universal container for small
quantities
⚫ For larger quantities 250 ml wide
mouthed screw-capped bottles are
convenient
For sputum:-
• Universal container should not
be used
• Squat ,wide-mouthed disposable
containers should be used

11. For blood:-
• Without anticoagulant for
serological examination
• With EDTA for parasitological
examination
 BLOOD CULTURE BOTTLE:
• This must be at least large
enough to hold 50ml of liquid
medium ,with which it is issued
from laboratory ,plus 5-10ml of
patient’s blood

12. For serous fluids:-
• Universal container
• Addition of 0.3ml of 20% solution
sodium citrate to the container prior to
autoclaving (with the cap fitted)
is recommended for collection of
fluids that may coagulate on standing
• This avoids difficulty in performing cell
counts or centrifuging procedure with
such fluids

13. Swabs:-
Swabs suitable for taking
Specimens of exudates from the
throat, nostril ,
ear , skin, wounds and other
accessible lesions consist of a sterile
pledget of absorbent material, usually
cotton-wool or synthetic fiber,
mounted on a thin wire of stick
Swabs for special purpose:
 Baby swabs
 Pernasal swabs
 Post-nasal swabs
 Laryngeal swabs
 High vaginal and cervical swabs
 Serum coated cotton wool swab

14.  Containers of anaerobic
specimens:
 Syringe and needle for aspiration.
 Tube or vial contains semi-solid holding medium an
atmosphere of 5% CO2 ,a reducing agent, tube used for
putting up the swab.
 Readymade swabs in a plastic tube or jacket and
containing either Cary-Blair , Amies transporter pre-
reduced (PRAs) medium id used.
 Plastic pouch or Bio-bag (transparent) containing a CO2
generating system, palladium catalyst and an anaerobic
indicator can also be used.

15. EYE:
Various specimens collected are:
A. specimens:
1.Conjunctival:-
 Container:
• Aerobic swab moistened with
Stuart’s or Amie’s medium
 Collection:
• Obtained from superior and inferior tarsal conjunctiva
• Specimen of both eyes with separate swabs by rolling swab over
each conjunctiva
• If a viral culture is requested ; a second
specimen is collected
• For Chlamydia culture swabs are taken with a
dry calcium alginate swab

16.  Transport :
• Within 24hrs/RT
• For viral culture place in viral transport media and
deliver promptly to laboratory or refrigerated
for a short time and then transport on wet ice
• For Chlamydia place in 2-Sp transport medium
2. Corneal scrapings:
 Container:
Bedside inoculation of BA,CA,SDA,7H10,Thio
 Patient preparation:
Clinician should instill local anesthetic before collection
 Collection:
By using heat sterilized platinum spatula or calcium
alginate- tipped swab dipped in sterile trypticase soya
broth
 Transport:
Immediately/RT

17. 3. Anterior chamber and vitreous cultures:
Collection:
Aspiration is carried out with a tuberculin
syringe fitted with a
• 25-27 gauge needle for the aqueous
• 20-21 gauge needle for vitreous
aspiration
Transport:
Immediately/RT

18. EAR:
1. Inner ear:
 Container:
• Sterile , screw-cap tube or
anaerobic transporter
 Patient preparation:
• Clean ear canal with mild soap
solution before puncture of the
ear drum
 Collection:
⚫ Aspirate material behind drum with syringe if ear drum is
intact; use swab to collect material from ruptured
eardrum
 Transport:
• Immediately/RT

19. 2. Outer ear:
Container:
• Aerobic swab
moistened with
Stuart's or Amie’s
medium
Patient preparation:
• Wipe away crust with
sterile saline
Collection:
• Firmly rotate swab in outer canal
Transport:
• Within 24hrs/RT

20. RESPIRATORY
TRACT(RT):
⚫Collection of specimen in the case of RTI
poses a number of problems
because , there is enormous
commensal flora that colonizes this
tract.
⚫Therefore, the specimen collection is
very crucial and specially in case of viral
infections of RT.
⚫One has to avoid contamination of the
specimens.
⚫RT is broadly divided into:

21. A . Upper RT:
Container:
• Swab moistened with Stuart’s or Amie’s medium
Collection:
1.Oral swab:
• Remove the oral secretions or debris
from the surface of lesion with swab and discard
• Using 2nd swab ,vigorously specimen the
lesion avoiding any areas of normal tissue
2. Nasal swab:
• Use swab moistened with sterile
saline.
• Insert approx. 2cm into nares
• Rotate swab against nasal mucosa

22. 3. Nasopharyngeal:
A. Swabs:
• To collect nasopharyngeal cells, all mucus is
removed
• Small flexible nasopharyngeal swab is inserted along
the nasal septum to the posterior pharynx
• Rotate slowly for 5 sec. against the mucosa
several times
B. Aspirate :
• Is collected with a plastic tube attached to 10 ml
syringe or suction catheter
C. Washings:
• Is obtained with a rubber suction bulb by instilling and
withdrawing 3-7 ml of sterile buffer saline

23. 4.Laryngeal swab:
• Before use the swab is moistened with sterile
D/W
• Patient is made sit and holding the tongue
fully protruded
• with help of a piece of gauge, pass the swab
back through the mouth wire mid-line and
downwards over the epiglottis into larynx where
it should induce reflex coughing that will expel
sputum onto swab
• Withdraw the swab and replace it in its tube for
delivery to the laboratory

24. 5. Throat swab:
• Depress the tongue with a tongue
depressor
• Introduce the swab between the tonsillar
pillars and behind the uvula without touching
the lateral walls of the buccal cavity
• Swab back and forth across
the posterior pharynx
• Any exudates or membrane should be taken for specimen
 Transport:
• Within 24hrs/RT

25. B. Lower RT:
 Container:
• Sterile screw-top container
 Collection:
1.Sputum:
Patient preparation:
Ask patient to brush teeth and
then rinse or gargle with water
before collection
• Collected early in the
morning before eating
• make collection in a
disposable wide mouthed
screw-capped sterile plastic
container of about
100ml capacity

26. • Instruct to wait until he/she feels material
coughed into his/her throat
• Then work it forward into mouth and spit it
directly into container
• Should be collected before starting
antimicrobial chemotherapy
2.Transtracheal aspiration(TTA):
• Obtained by inserting a small plastic
catheter into the trachea via a needle
previously inserted through the skin and
cricothyroid membrane
• This technique is rarely used any more

27. 3.Bronchioalveolar lavage (BAL):
• 30-50 ml of physiological saliva is
injected through a fiberoptic
bronchoscope .
• the saliva is then aspirated
4.Bronchial brush:
• Is collected via a protected
catheter bronchial brush as part of
a bronchoscopy examination
5.Gastric lavage:
• In the morning before the patient
has taken anything but after a
bout of coughing and swallowing
, aspirate the fasting stomach
contents with a Ryle’s tube
 Transport:
• Within 24hrs/RT

28. BODY FLUIDS:
1.Cerebrospinal fluid:
Container:
• Sterile screw-cap tube
Patient preparation:
• Disinfect skin before aspirating specimen
Collection:
• Lumbar puncture to collect the CSF for
examination to be collected by Physician
trained in procedure with aseptic
precautions to prevent introduction of
Infection.

29. • The trained physician
will collect only 3-5 ml
into a labeled sterile
container
• The fluid to be
collected at the rate
of 4-5 drops per second.

30. ⚫The best site for puncture is inter
space between 3 and 4 lumbar
vertebrae
• The Physician should wear sterile
gloves and conduct the procedure with
sterile precautions, The site of
procedure should be disinfected and
sterile occlusive dressing applied to the
puncture site after the procedure.

31. Transportation to Laboratory:
The collected specimen
of CSF to be dispatched
promptly to Laboratory ,
delay may cause death
of delicate pathogens,
e.g. Meningococci and disintegrate
leukocytes

32. Preservation of CSF:
It is important when
there is delay in
transportation of
specimens to Laboratory
do not keep in
Refrigerator, which tends
to kill H. Influenza
 If delay is anticipated
 leave at Room
Temperature.

33. 2.Pleural/Peritoneal/Pericardial/
Synovial fluid:
Container:
• Sterile screw-cap tube or anaerobic
transporter
Patient preparation:
• Disinfect skin before aspirating with 2%
iodine tincture
Collection:
• Obtained via percutaneous needle
aspiration or surgery
Transport:
• Immediately/RT

34. BLOOD:
Container:
• Blood culture media set(aerobic and anaerobic
bottle)
or vacutainer tube with SPS
Patient preparation:
•Disinfect venipuncture site
with 70% alcohol and
disinfectant such as betadine

35. Collection:
• Select the vein from which blood is to
be drawn
• Disinfect the venipuncture site
• Allow it to dry
• With precautions to avoid touching
and recontaminating the
venipuncture Site , take the
specimen of blood and put it
immediately through the hole in the cap of bottle
Volume of blood:
• In adult 5-10ml
• In children 1-5ml
Transport:
• Within 2hrs/RT

36. Gastrointestinal tract(GIT):
1.Stool:
 Container:
• Clean leak-proof container
 Collection:
•Pass stool directly into a sterile, wide-mouth, leak proof
container with a tight fitting lid.
•Pass stool into a clean, dry bedpan, and transfer into a
sterile leak proof container with a tight fitting lid.
⚫ Stool for ova and parasites should be placed in preservative
immediately after collection.
 Transport:
• Within 24hrs/4 °C
• If delay is unavoidable and particularly when the weather is warm
collect the specimens in a container holding 6 ml buffered glycerol
saline transport medium

37. All enteric organisms
All enteric organisms
All enteric organisms
All enteric organisms
except
Vibrios
Campylobacter
Vibrios
Cary-Blair
Stuart
Amies
Buffered glycerol
saline
Alkaline peptone
water
V-R fluid Vibrios
Transport media for stool specimens

38. 2.Rectal swab:
Container:
• Swab placed in enteric transport
medium
Collection:
⚫Pass the tip of a sterile swab
approximately 1 inch beyond the anal
sphincter.
⚫Carefully rotate the swab to sample
the anal crypts and withdraw the
swab. Place the swab in transport
medium.
Transport:

39. 3.Duodenal aspirates:
 Container:
• Sterile, screw-cap tube
 Patient preparation:
• Collect in early AM before patient eats or gets out
of bed.
 Collection:
• Ask the patient to swallow a weighted gelatin
capsule containing a tightly wound length of string,
which is left protruding from the mouth and taped to
the cheek
• After a predetermined period , during which the
capsule reaches the duodenum and dissolves, the
string now covered with duodenal contents is
retracted .
 Transport:

40. URINARY TRACT INFECTION(UTI):
1.Urine:
 Container:
• Sterile, screw-cap container
 Patient preparation:
Females:
• Clean area with soap and water, then rinse with
water, hold labia apart and begin voiding in
commode; after several ml have passed, collect
midstream
Males:
• Clean glans with soap and water, then rinse with
water, retract foreskin; after several ml have

41. Collection:
• after several ml have
passed, collect midstream
in a urine container
Transport:
• Within 24hrs/4°C
2.Catheter specimen of urine (CSU):
 Container:
• Sterile, screw-cap container
 Patient preparation:
• Clean urethral area (soap and water) and rinse
(water)

42. Collection:
• Insert catheter into bladder
• Allow first 15ml to pass
• Then collect remainder
Transport:
• Within 24hrs/4°C
3.Suprapubic bladder aspiration:
• It is used primarily for neonates and small
children but may be safely used in adults
• A full bladder is required for this
• Overlying skin id disinfected
• Bladder is punctured above the symphysis
pubis with a 22-gauge needle on a syringe
• About 10ml of urine is aspirated

43. HAIR,NAILS, OR SKIN SCRAPINGS
(FOR FUNGUS CULTURE)
Container:
• Clean, screw-top tube
Patient preparation:
• Nails or skin: wipe with 70% alcohol
Collection:
• Hair: Collect hair with intact shaft
• Nails: Send clippings of affected area
• Skin: Scrape skin at leading edge of lesion
Transport:
• Within 24hrs/RT

44. ABSCESS:
(also lesions, wounds, pustule, ulcer)
A . Superficial:
 Container:
•Anaerobic swab
moistened with Stuart’s or
Amie’s medium
 Patient preparation:
•Wipe area with sterile saline or
70% alcohol
 Collection:
• Swab along the leading edge of wound
 Transport:
• Within 24hrs/RT

45. B . Deep:
 Container:
• Anaerobic transporter
 Patient preparation:
• Wipe area with sterile saline or 70%
alcohol
 Collection:
• Aspirate material from wall or excise
tissue
 Transport:
• Within 24hrs/RT

46. Genital tract
 A . Females:
1.Cervical swab:
 Container:
• Swab moistened with
Stuart’s or Amie’s medium
 Patient preparation:
• Remove mucus before
• collection of specimen
 Collection:
• Swab deeply into
endocervical canal
 Transport:
• Within 24hrs/RT

47. 2 . High vaginal swab:
Container:
• Swab moistened with Stuart’s or Amie’s medium
• Or JEMBEC transport system
Patient preparation:
• Remove exudates
Collection:
• Swab secretions and mucous membrane of vagina
Transport:
• Within 24hrs/RT

48. 3 . Urethral swab:
Container:
• Swab moistened with Stuart’s or Amie’s medium
Patient preparation:
• Remove exudates from urethral opening
• Collection:
• Collect discharge by massaging urethra
against pubic symphysis
• Or insert flexible swab 2-4cm into urethra
and rotate swab for 2 sec.
• Collect at least 1 hr after patient has
urinated
Transport:
• Within 24hrs/RT

49. B . Males:
1.Prostrate:
Container:
• Swab moistened with Stuart’s or Amie’s medium
• Or sterile screw-cap tube
Patient preparation:
• Clean glans with soap and water
Collection:
• Collect secretion on swab or
• In tube
Transport:
• Within 24hrs/RT for swabs
• Immediately/RT if in tubes

50. 2 . Urethra:
Container:
• Swab moistened with Stuart’s or Amie’s medium
• Or JEMBEC transport system
Collection:
• Insert flexible swab 2-4cm into urethra and rotate for 2
sec.
• Or collect discharge on JEMBEC transport system
Transport:
• Within 24hrs/RT for swab
• Within 2hrs for JEMBEC transport system

51. REFRENCES:
 Specimen Collection In Clinical
Microbiology
Dr. V. L.Malhotra, Dr. Neelam Khandpur
 Bailey And Scott's Diagnostic Microbiology
(12th Edition)
 Koneman’s Colour Atlas Of Diagnostic
Microbiology (6th Edition)
 Textbook Of Microbiology- Ananthanarayan
And Paniker’s(8th Edition)
 MackieAnd McCartney Practical
Microbiology(14th Edition)
 Internet