Collection of biological specimens for microbiology tests

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