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Collection and transport


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jitendra kumar pandey,mgm medical college,mumbai

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Collection and transport

  2. 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. 3. General guidelines forspecimen 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. 4. An Ideal Request form Name xxxx Age Sex IP/ OP No xyz Time Date Ward xx123 Urgent / Routine Nature of specimen Investigation needed Doctor/Staff Contact No 1234567
  5. 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. 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. 7.  Triple packaging system
  8. 8. Criteria for rejection ofspecimens: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. 9. Containers and swab forthe collection ofspecimens:Containers:For faeces:-• Universal container• Spoon attached to the inside of the screw cap
  10. 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. 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. 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. 13. Swabs:-Swabs suitable for taking Specimensof exudates from the throat, nostril ,ear , skin, wounds and other accessiblelesions consist of a sterile pledget ofabsorbent material, usually cotton-woolor 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. 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. 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. 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 medium2. 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. 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. 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. 19. 2. Outer ear: Container:• Aerobic swab moistened with Stuarts or Amie’s medium Patient preparation:• Wipe away crust with sterile saline Collection:• Firmly rotate swab in outer canal Transport:• Within 24hrs/RT
  20. 20. RESPIRATORYTRACT(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. 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 tissue2. Nasal swab:• Use swab moistened with sterile saline.• Insert approx. 2cm into nares• Rotate swab against nasal mucosa
  22. 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 timesB. Aspirate :• Is collected with a plastic tube attached to 10 ml syringe or suction catheterC. Washings:• Is obtained with a rubber suction bulb by instilling and withdrawing 3-7 ml of sterile buffer saline
  23. 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. 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. 25. B. Lower RT: Container:• Sterile screw-top container Collection:1.Sputum: Patient preparation:Ask patient to brush teethand then rinse or gargle withwater 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. 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 chemotherapy2.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. 27. 3.Bronchioalveolar lavage (BAL):• 30-50 ml of physiological saliva is injected through a fiberoptic bronchoscope .• the saliva is then aspirated4.Bronchial brush:• Is collected via a protected catheter bronchial brush as part of a bronchoscopy examination5.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. 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. 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. 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. 31. Transportation to Laboratory: The collected specimenof CSF to be dispatchedpromptly to Laboratory ,delay may cause deathof delicate pathogens,e.g. Meningococci and disintegrate leukocytes
  32. 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. 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. 34. BLOOD: Container:• Blood culture media set(aerobic and anaerobic bottle)or vacutainer tube with SPS Patient preparation:• Disinfect venipuncture sitewith 70% alcohol anddisinfectant such as betadine
  35. 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. 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. 37. Transport media for stool specimensCary-Blair All enteric organismsStuart All enteric organismsAmies All enteric organismsBuffered glycerol All enteric organismssaline except Vibrios CampylobacterAlkaline peptone VibrioswaterV-R fluid Vibrios
  38. 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. 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. 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. 41.  Collection:• after several ml have passed, collect midstream in a urine container Transport:• Within 24hrs/4°C2.Catheter specimen of urine (CSU): Container:• Sterile, screw-cap container Patient preparation:• Clean urethral area (soap and water) and rinse (water)
  42. 42.  Collection:• Insert catheter into bladder• Allow first 15ml to pass• Then collect remainder Transport:• Within 24hrs/4°C3.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. 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. 44. ABSCESS:(also lesions, wounds, pustule, ulcer)A . Superficial: Container:• Anaerobic swabmoistened with Stuart’s orAmie’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. 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. 46. Genital tractA . 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. 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. 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. 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. 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. 51. REFRENCES: Specimen Collection In Clinical Microbiology Dr. V. L.Malhotra, Dr. Neelam Khandpur Bailey And Scotts Diagnostic Microbiology (12th Edition) Koneman’s Colour Atlas Of Diagnostic Microbiology (6th Edition) Textbook Of Microbiology- Ananthanarayan And Paniker’s(8th Edition) Mackie And McCartney Practical Microbiology(14th Edition) Internet