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Collection of biological specimens for microbiology tests


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main principles of specimen collection for microbiology tests with examples of collection rules and techniques for various types of samples

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Collection of biological specimens for microbiology tests

  1. 1. Collection and transport of biological specimens
  2. 2. Biological specimens Depending on source: • sterile collection sites: – Blood, CSF, urine • contaminated collection sites: – Faeces, naso-pharyngeal secretion, pus, vaginal secretion + specimens from sterile collection sites which may be contaminated during elimination e.g. sputum, urine
  3. 3. Parameters to be considered when collecting biological specimens • WHAT: choice of biological specimen depending on clinical stage • WHEN: optimal moment of collection; maximum time to reach the laboratory • HOW: collection procedure (avoid contamination of specimen); instruments (sterile !!); manipulation and packaging (no contamination of staff and environment) • HOW MUCH: adequate quantity for required tests
  4. 4. Minimal Information in Request form • About patient: ID, age, gender • About disease: date of onset, suspected diagnosis/causative pathogen • About specimen: type of specimen, collection site, time of collection, time of shipment, storage conditions (if applicable) • About referring physician – contact data (name, phone no)
  5. 5. Microbiological tests: Most often referred specimens • Biological samples: secretions, excretions, tissues, organ fragments • Food samples • Pharmaceutic products, cosmetics • Environmental samples: water, air, soil
  6. 6. General requirements for collecting pharyngeal, naso-pharingeal exudate • For the patient: – in the morning, before feeding, before brushing teeth; alternatively: at least 4 hours since last meal & teeth brushing – No mouth rinse, no chewing gum! – No antibiotics during the last 7-10 days • For medical staff: – Wear gloves, face protection (mask, eye protection/face shield), protective lab coat
  7. 7. Collection of pharyngeal exudate • Dacron or Rayon swab • Tongue blade & good light • Insert swab behind uvula without touching it • Swab tonsils, posterior pharynx + lesions (if any) • Avoid touching tongue, cheeks, teeth • Place swab in sterile tube • Transport to lab (RT/2-8°C)
  8. 8. Collection of pharyngeal exudate
  9. 9. Collection of nasal/nasopharyngeal exudate • Head of patient imobilised in neck extension • Sterile swab gently inserted through nostril along nasal floor until reaching posterior pharingeal wall • Rotate swab, withdraw slowly + reinsert and repeat steps • Take out and insert into sterile tube • Send to lab
  10. 10. Collection of sputum • Challenging! – must avoid contamination of sputum with saliva and secretions from upper air ways Optimal moment: in the morning (higher amount of sputum secreted during the night and stagnant in lower respiratory ways) Indirect method: • Patient energically rinses mouth with saline solution • Coughs and expectorates in sterile container (Petri dish) Direct method: • Bronchoscopy / tracheal punctioning
  11. 11. Collection of Blood • Normally sterile biological product • Collection technique depends on the required tests: – A. bacteriology = hemoculture – B. Serology
  12. 12. A. Blood collection for hemoculture Blood injected in 2 sets of sealed bottles containing liquid culture medium for aerobic and anaerobic bacterial growth
  13. 13. Collection of blood for hemoculture • Wear gloves + PPE • Thoroughly wipe skin with antiseptic (chlorhexidine, iodine, alcohol) • During 3 hours, draw blood by venipuncture from up to 3 different sites at 1 hour interval (3 sets of 2 bottles each) – around 5 ml blood per bottle • After drawing the blood, dispose of the syring needle and attach new, sterile needle • Disinfect cap of each culture medium bottle and inject 5 ml blood/bottle
  14. 14. Collection of blood for hemoculture
  15. 15. Automated systems for detection of bacteria in blood and other normally sterile body fluids
  16. 16. B. Blood collection for serology • similar PPE used by person collecting sample (gloves, lab coat, eye protection, etc) • Thorough skin decontamination with antiseptic • Blood drawn by venipuncture with: • sterile syringe and needle and injected/inserted in sterile container • Vacuum collecting system (tube + needle): blood drawn by vacuum into tube containing clot activating substance (facilitates clot formation & separation of serum)
  17. 17. B. Blood collection for serology
  18. 18. Collection of Pus • Composition: white blood cells, microbes, cell debris, fibrin Closed purulent lesions (abscesses): • surgical collection: – rigurous cleaning and disinfection of skin (iodine) – Incision and aspiration of pus Open lesions: • Cleaning and disinfection of skin around lesion (iodine) • Collection of pus with sterile swab / loop
  19. 19. Collection of stool (faeces) • Disposable stool collection containers (simple / with transportation medium Carry Blair: non-nutritive medium which prevents overgrowth of Enterobacteriaceae but preserves viable enteric pathogens (Salmonella, Shigella, Vibrio, etc)
  20. 20. Collection of urine When?: - in the morning (first miction) How?: - clean uro-genital area - eliminate first flow - collect middle flow in sterile container Send to lab immediately or store at 2-8°C
  21. 21. Collection of cerebrospinal fluid (CSF) Lumbar punction (spinal tap) • patient lies on the side, knees pulled up toward chest, chin tucked downward • back cleaned and disinfected (iodine) + health care provider injects local anesthetic into lower spine • spinal needle inserted into lower back area • needle properly positioned, CSF pressure measured and sample collected in sterile tube • needle removed, area cleaned, bandage placed over puncture site