This document provides guidelines for collecting, handling, transporting, and labeling microbiological samples for laboratory testing. It discusses appropriate collection methods and media for different sample types including blood, cerebrospinal fluid, stool, respiratory, and post-mortem samples. Guidelines are also provided on biosafety procedures, case investigation forms, and criteria for rejecting samples. The key aspects covered are collection of adequate samples, use of appropriate transport media, maintaining proper transport conditions, completing necessary documentation, and following biosafety protocols.

1. MICROBIOLOGY (NRS 212)
Sample collection and shipping
Collection, Labelling and Transportation of
Microbiological samples

2. Collection and transport of microbiological
samples

3. • Collection of adequate and appropriate specimens
• Sufficient documentation
• Biosafety and decontamination
• Correct packaging
• Rapid transport
• Choice of a laboratory that can accurately perform the tests
• Timely communication of results
• Advance planning
Successful laboratory investigations:-

4. Consider differential diagnoses:-
• Decide on test(s) to be conducted
• Decide on clinical samples to be collected to conduct these tests
• Consultation between microbiologist, clinicians and epidemiologist
Specimen collection: key issues

5. • Allows organisms (pathogens and contaminants) to survive.
• Non-nutritive - does not allow organisms to proliferate.
• For bacteria – i.e., Cary Blair
• For viruses - virus transport media (VTM)
Transport medium:-

6. Collection:-
Capillary blood from finger prick
• make smear
• fix with methanol or other fixative
Handling and transport:-
Transport slides within 24 hours
Do not refrigerate (can alter cell morphology)
Blood for smears:-

7. Collection
• Venous blood
• infants: 0.5 – 2 ml
• children: 2 – 5 ml
• adults: 5 – 10 ml
• Requires aseptic technique.
• Collect within 10 minutes of fever.
• if suspect bacterial endocarditis: 3 sets of blood culture
Blood for cultures:-

8. Handling and Transport:-
Blood for cultures Collect into bottles with
infusion broth
• change needle to inoculate the broth
Transport upright .
• prevents hemolysis
Blood for cultures:-

9. Collection
Venous blood in sterile test tube
• Let clot for 30 minutes at surrounding temperature
• glass better than plastic
Handling
Place at 4-8oC for clot retraction for at least 1-2 hours
Centrifuge at 1500 RPM for 5-10 min
• separates serum from the clot
Transport
4-8oC if transport lasts less than 10 days
Freeze at -20oC if storage for weeks or months before processing
and shipment to reference laboratory.
Avoid repeated freeze-thaw cycles
• destroys IgM
To avoid hemolysis: do not freeze unseparated blood
Serum:-

10. Collection procedure:-
• Lumbar puncture
• Sterile tubes
• Aseptic conditions
• Trained person
Cerebrospinal fluid (CSF):-

11. CSF
Handling and transportation
Bacteria
• preferably in Transporter -isolate medium,
pre-warmed to 25-37°C before inoculation
OR
• transport at surrounding temperature (relevant pathogens
do not survive at low temperatures)
Viruses
• transport at 4-8oC (if up to 48hrs or -70oC for longer
duration)

12. Collection:
Freshly passed stool samples
• avoid specimens from a bed pan
Use sterile or clean container
• do not clean with disinfectant
During an outbreak - collect from 10-20 patients
Stool samples:-

13. Advantage:-
• suitable
• Adapted to small children, impaired patients and other situations
where voided stool sample not feasible (possible)
Disadvantage:-
• No macroscopic assessment possible
• not recommended for viruses
Rectal swabs:-

14. Timing
 within 48 hours of onset
Sample amount
 5-10 ml fresh stool from patients (and controls)
Methods
 fresh stool unmixed with urine in clean, dry and sterile container
Storage
 refrigerate at 4oC; do not freeze
 store at -15oC - for Ag detection, polymerase chain reaction (PCR)
Transport
 4oC (do not freeze); dry ice for (Ag detection and PCR)
Stool samples for viruses:-

15. Timing
 during active phase
Sample amount and size
 fresh sample and two swabs from patients, controls and carriers (if
indicated)
Method
 Cary-Blair medium
 For Ag detection/PCR – no transport medium
Storage
 refrigerate at 4oC if testing within 48 hours, -70oC if longer; store at -
15oC for Ag detection and PCR
Transport
 4oC (do not freeze); dry ice for (Ag detection and PCR)
Stool samples for bacteria:-

16. Timing
 as soon as possible after onset
Sample amount and size
 at least 3 x 5-10 ml fresh stool from patients and controls
Method
 Mix with 10% formalin or polyvinyl chloride, preservative
 Unpreserved samples for Ag detection and PCR
Storage
 refrigerate at 4oC; store at -15oC for Ag detection and
PCR
Transport
 4oC (do not freeze); dry ice for (Ag detection and PCR)
Stool samples for parasites:-

17. • Hold tongue away with tongue
depressor
• Locate areas of inflammation and
exudate in (posterior pharynx,
tonsillar region of throat behind
uvula)
• Avoid swabbing soft palate (uvula);
do not touch tongue
• Rub area back and forth with cotton
or Dacron swab.
WHO/CDS/EPR/ARO/2006.1
Throat swab (posterior pharyngeal swab):-
Dacron swab

18. • Tilt (slope) head backwards
• Insert flexible fine-shafted polyester
swab into nostril and back to
nasopharynx
• Leave in place a few seconds
• Withdraw slowly; rotating motion
Nasopharyngeal swab:-

19. • Tilt (slope) head slightly backward.
• Instill (inject) 1-1.5 ml of VTM (Viral
Transport Medium) /sterile normal saline
into one nostril.
• Use aspiration device.
• Insert silicon catheter in nostril and
aspirate the secretion gently by suction
in each nostril
Naso-pharyngeal aspirate:-

20. Collection
• Instruct patient to take a deep breath and cough up sputum directly
into a wide-mouth sterile container.
• avoid saliva or postnasal discharge.
• 1 ml minimum volume
Sputum:-

21. Handling and Transport:-
- All respiratory specimens except sputum are transported
in appropriate media.
• bacteria: Amie’s or Stuart’s transport medium
• viruses: viral transport medium (VTM)
- Transport as quickly as possible to the laboratory to
reduce overgrowth by oral flora
- For transit periods up to 24 hours
• surrounding temperature for bacteria
• 4-8°C for viruses
Respiratory samples:-

22. Collection:-
Biopsy relevant tissues
• place in formalin for histopathology
• place in transport medium for microbiological testing
• place in sterile saline for isolation of viral pathogens
Post-mortem samples:-
Handling and transportation:-
• Fixed specimens can be transported at surrounding
temperatures.
• Transport specimens in transport media within 24h at
surrounding temperature.
• Transport specimens in sterile saline at 4-8oC within 48h.

23. • Patient’s name
• Clinical specimen
• Unique ID number (Research/Outbreak)
• Specimen type
• Date, time and place of collection
• Name/ initials of collector
Labeling specimens:-

24. Label slides individually:
• use glass marking pencil
• ensure markings don’t interfere with staining process
Each slide should bear:
• Patient name
• Unique identification number
• Date of collection
Glass slides for microscopy:-

25. Patient information:-
 age (or date of birth), sex, complete address
Clinical information:-
 date of onset of symptoms, clinical and immunization history, risk
factors or contact history where relevant, anti-microbial drugs taken
prior to specimen collection
Laboratory information:-
 acute or recovering specimen
 other specimens from the same patient
Receiving laboratory records:
 Date and time when specimen was received
 Name and initials of the person receiving specimen
 Record of specimen quality
(Line listing – if large number of patients)
Case investigation form:-

26. • Use single use equipment
• Disinfect
• Work in a clean, specific area
Biosafety: protect the patient:-

27. Use personal protective equipment
• disposable gloves
• laboratory coats / gown
• mask
• protective eyewear .
• Face shields if procedure is likely to generate aerosols.
Note:-
• If no sharps container: collect sharps immediately to prevent needle-
stick injury
• First aid kit readily accessible
• Do not reuse contaminated equipment
Biosafety: protect yourself:-

28. • Package samples appropriately for transport.
• Decontaminate spills - 10% bleach wash in soapy water before re-
use, sterilize if necessary
• Place waste in leak-proof biohazard bags - ensure safe final
management of waste
• Protect cleaning/decontamination personnel with protective
coat, thick rubber gloves
Biosafety: protect others, the environment:-

29. • Mismatch of information on the label and the request.
• Inappropriate transport temperature
• Excessive delay in transportation
• Inappropriate transport medium
1. specimen received in a fixative
2. dry specimen
3. sample with questionable relevance
• Insufficient quantity.
Criteria for rejecting samples:-

30. THANKS