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Collection of biological specimens for microbiology tests

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Dana Sinziana Brehar-Cioflec
Dana Sinziana Brehar-Cioflec

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 and transport of biological specimens
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
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
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)
Microbiological tests: Most often referred specimens • Biological samples: secretions, excretions, tissues, organ fragments • Food samples • Pharmaceutic products, cosmetics • Environmental samples: water, air, soil
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
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)
Collection of pharyngeal exudate
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
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
Collection of Blood • Normally sterile biological product • Collection technique depends on the required tests: – A. bacteriology = hemoculture – B. Serology
A. Blood collection for hemoculture Blood injected in 2 sets of sealed bottles containing liquid culture medium for aerobic and anaerobic bacterial growth
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
Collection of blood for hemoculture
Automated systems for detection of bacteria in blood and other normally sterile body fluids
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)
B. Blood collection for serology
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
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)
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
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

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Collection of biological specimens for microbiology tests

  • 1. Collection and transport of biological specimens
  • 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. 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. 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. Microbiological tests: Most often referred specimens • Biological samples: secretions, excretions, tissues, organ fragments • Food samples • Pharmaceutic products, cosmetics • Environmental samples: water, air, soil
  • 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. 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)
  • 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. 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. Collection of Blood • Normally sterile biological product • Collection technique depends on the required tests: – A. bacteriology = hemoculture – B. Serology
  • 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. 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. Collection of blood for hemoculture
  • 15. Automated systems for detection of bacteria in blood and other normally sterile body fluids
  • 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. B. Blood collection for serology
  • 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. 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. 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. 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