Collection and transport of specimen

Collection and transport of specimen for microbiological diagnosis

-Aims of the clinical microbiology laboratory

Ø  To provide accurate information about the presence or absence of microorganisms in a specimen

Ø  To provide information on the antimicrobial susceptibility of microorganisms isolated

Ø  To detect evidence of patient’s immune response

 Microbiological methods

Ø  Identification of microorganisms by isolation and culture

Ø  Identification of a specific microbial product

Ø  Detection of specific antibodies to a pathogen

Use of microbiology laboratory

Points to consider by the clinicians

Ø  Possible diseases?

Ø  Specimen/s that can give the diagnosis?

Ø  Tests to request on the specimen?

Ø  When to collect the specimen?

Ø  How to handle the specimen ?

Ø  Interaction with the microbiologist?

Specimen collection

   Selection of appropriate specimen

Ø  Relevant specimen

Ø  Instruction

Optimal time of collection

Ø  Culture: before antimicrobials

Ø  Stage of the disease: typhoid fever

Ø  Acute phase of illness: malaria, virus isolation

Ø  Serology: paired sera

Adequate quantity and number of specimens

Ø  Blood for culture

Ø  Sputum for Mycobacteria

Ø  Paired sera

Avoid contamination

Ø  From normal flora - mid stream urine

Ø  From external source

§  Sterile equipment

§  Aseptic technique

Specimens labelling and request forms

Ø  Proper labelling

Ø  Completed requisition forms

Ø  Necessary information

§  patient

§  clinical diagnosis

§  antimicrobial therapy

Transport to the laboratory

Ø  Rapid

Ø  In case of delay

§  Body fluids: never refrigerate

§  Urine/sputum: refrigerate

§  Use of transport medium

Ø  Direct inoculation bedside

§  Corneal scraping

§  Genital tract

Ø  Standard precautions

Ø  Communication with the microbiologist

Blood culture

Ø  Indications

Ø  Timing

Ø  Number of samples

Ø  Volume of blood

Ø  Sites

Ø  Skin antisepsis

Ø  Use of blood culture bottle

Ø  Antimicrobials

Throat swab

Ø  Sampling error

Ø  Role of Gram staining

§  Need of  special staining

§  special media

 Sputum

Ø  Instruction for collection

Ø  Minimise oropharyngeal and salivary contamination

Ø  Suitability for culture

Ø  Number of samples for Mycobacteria

Urine

Ø  Instruction for midstream urine

Ø  Significant bacteriuria

Ø  Suprapubic aspirate

Ø  Urine from catheter

Ø  Immediate transport

Ø  Sample for Renal tuberculosis

CSF and fluids from sterile sites

Ø  Aseptic collection

Ø  Adequate volume

Ø  Immediate transport

Ø  Need of

§  Special staining

§  Special media

Stool

Ø  Use of special medium

Ø  Microscopy

Ø  Multiple samples may be required

Ø  Immediate transport

Wound

Ø  Optimal sample

• Infected tissue
• Purulent material aspirate
• Sterile swab

•          Poor isolation

•          Not suitable for anaerobic culture

Genital secretion cultures

Ø  Gonococcus

§  Urethral discharge

§  Cervical swab

Ø  Microscopy

Ocular specimens

Ø  Immediate inoculation

Ø  Microscopy

Ø  Special preparation and medium

Errors that can occur pre analytically

Ø  Inappropriate specimen

Ø  Timing not optimum

Ø  Inadequate quantity

Ø  Inadequate number of samples

Ø  Antimicrobial therapy

Ø  No clinical information

Ø Contamination ,normal flora