Specimen collectionDR. MANAR AKAS

MICROBIOLOGY & IMMUNOLOGY

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Specimen collection: key issues

What is your differential diagnosis?

What test(s) you should conduct?

How to collect appropriate samples ?

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Successful laboratory investigationsAdvance 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

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Transport mediumAllows 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)

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specimens type

◦ Urine

◦ Stool

◦ Sputum

◦ Wound drainage/puss

◦ Blood

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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

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Stool SpecimenAnalysis 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

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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

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Stool samples for parasitesTiming

◦ 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

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Respiratory TractTests 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

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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

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Sputum collectionOrdered 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.

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Blood for smearsCollection

Capillary blood from finger prick

◦ make smear◦ fix with methanol

Handling and transportTransport slides within 24 hours

Do not refrigerate (can alter cell morphology)

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Blood for culturesCollection

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

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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

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Cerebrospinal fluid (CSF)

Collection

Trained person

Aseptic conditions Lumbar puncture

Sterile tubes

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CSFHandling 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)

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Labeling specimens

Patient’s name

Clinical specimen

Unique ID number

Specimen type

Date, time and place of collection

Name/ initials of collector

Thank you

Questions?

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