2. Specimen collection: key issues
What is your differential diagnosis?
What test(s) you should conduct?
How to collect appropriate samples ?
11/feb/2015 DR. MANAR 2
3. Successful laboratory investigations
Advance planning
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
11/feb/2015 DR. MANAR 3
4. Transport medium
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)
11/feb/2015 DR. MANAR 4
6. Why a urine
specimen
? Urinary Tract Infection (UTI)
◦ Frequency
◦ Urgency(An immediate
unstoppable urge to urinate)
◦ Dysuria (painful urination)
◦ Hematuria(blood in urine)
◦ Flank pain
◦ Fever
Culture = ? Bacteria growing
Sensitivity = which antibiotics are effective
Midstream Urine
Sterile Catheter Specimen
(never from bag)
Random
Clean
Female ?
Menstrual details
Tested for:
◦ Specific gravity
◦ pH
◦ Albumin
◦ Glucose
◦ Microscopic exam
To lab 15-20min post collection
11/feb/2015 DR. MANAR 6
7. Stool Specimen
Analysis of fecal material can detect pathological conditions i.e:
infection, hemorrhage, tumors.
Tests
◦ Occult Blood
◦ Bacteria
◦ Ova & Parasites
Note the:
1-Color
◦ Melena
(black stools)
2-Odor
3-Consistency
Medical aseptic technique
To lab on time
Labelling /Documentation
11/feb/2015 DR. MANAR 7
8. Stool samples for bacteria
Timing
◦ during active phase
Method
◦ Cary-Blair medium
◦ For Ag detection/PCR – no transport medium
Storage
◦ refrigerate at 4oC if testing within 48 hours, store at -15oC for Ag detection and PCR
Transport
◦ 4oC (do not freeze); dry ice for Ag, PCR detection
11/feb/2015 DR. MANAR 8
9. Stool samples for parasites
Timing
◦ as soon as possible after onset
Sample amount and size
◦ at least 3 x 5-10 ml fresh stool from patients and controls
Storage
◦ refrigerate at 4oC; store at -15oC for Ag detection and PCR
Transport
◦ 4oC (do not freeze); dry ice for antigen detection and PCR
11/feb/2015 DR. MANAR 9
10. Respiratory Tract
Tests to determine infection
◦ Throat cultures
◦ Sputum specimens
Upper respiratory/ throat infections
Throat swabs
◦ before meal or 1 hr after meal
◦ Wash hands, glove
◦ Tilt head backward
◦ “ah” ( if pharynx not visualized, tongue depressor, anterior 1/3 of tongue)
◦ Don’t contaminate
11/feb/2015 DR. MANAR 10
11. Nose & Throat cultures
Nose, Oropharynx & tonsillar
Sterile swab
Insert swab into pharyngeal region
Take swab from reddened areas/ exudate
Culture determines pathogenic microorganisms
Sensitivity determines the antibiotics to which the
microorganisms are sensitive or resistant
11/feb/2015 DR. MANAR 11
12. Sputum collection
Ordered to identify organisms growing in sputum
Culture & Sensitivity
AFB (acid fast bacilli)
3samples in 3 consecutive days, early morning
◦ Cough effectively,avoid postnasal discharge and saliva
◦ 1 ml minimum volume
Record
◦ Color
◦ Consistency (thickness)
◦ Amount
◦ Odor
◦ Document date & time sent to lab.
11/feb/2015 DR. MANAR 12
13. Blood for smears
Collection
Capillary blood from finger prick
◦ make smear
◦ fix with methanol
Handling and transport
Transport slides within 24 hours
Do not refrigerate (can alter cell morphology)
11/feb/2015 DR. MANAR 13
14. Blood for cultures
Collection
Requires aseptic technique
Venous blood
◦ infants: 0.5 – 2 ml
◦ children: 2 – 5 ml
◦ adults: 5 – 10 ml
Collect within 10 minutes of
fever
◦ if suspect bacterial endocarditis:
3 sets of blood culture
11/feb/2015 DR. MANAR 14
15. Blood for cultures
Handling and Transport
Collect into bottles with infusion broth
◦ change needle to inoculate the broth
Transport upright with cushion
◦ prevents hemolysis
Wrap tubes with absorbent cotton
Travel at ambient temperature
Store at 4oC if can’t reach laboratory in 24h
11/feb/2015 DR. MANAR 15
17. CSF
Handling and transportation
Bacteria
◦ Medium pre-warmed to 25-37°C before inoculation
OR
◦ transport at ambient temperature (relevant pathogens do not
survive at low temperatures)
Viruses
◦ transport at 4-8oC (if up to 48hrs or -70oC for longer duration)
11/feb/2015 DR. MANAR 17
