Clinical Specimen Selection, Collection, Transport, and Storage for Microbiological Diagnosis

General Considerations in Specimen Collection

•  Collection before antibiotic therapy whenever possible.
•  Asepsis in collection of all specimens.
•  Consider stage of disease.
•  Use of proper containers and/or transport media.
•  Deliver specimen promptly.

The vitals for specimen collection:

Requisition

The following details should be included in the laboratory request, or “lab slip”:

•  Patient name
•  Patient age and sex
•  Patient room number or address
•  Date and hour of specimen collection
•  Clinical diagnosis, special culture request, relevant patient history
•  Special procedures used in obtaining specimen
•  Antimicrobials, if any, patient is receiving

Specimen selection and Collection:

•  Use of sterile containers
• Transport medium in case of delay
• Aseptic collection
• Stool mixed with urine is not acceptable
•  Prompt delivery to the laboratory if specimen contains blood as soon as possible.
• The best way to obtain anaerobic cultures is to aspirate abscess fluid using a sterile syringe and needle. Use gassed tubes for swabs.
•  Sputum samples not saliva should be collected.
• If pulmonary tuberculosis suspected, up to three specimens to detect AFB
•  When pneumonia or bronchopneumonia is suspected, prompt sputum lab delivery.
•  Bronchial brushings are preferable to washings because washings are dilute
• To prevent contamination, use a nasopharyngeal swab through the throat or the nose.
•  For Bordetella pertussis, Streptococcus pneumoniae, and Neisseria meningitides, nasopharyngeal secretion aspiration.
• The collection of clean-catch urine samples.  Preserve with boric acid
•  Catheter tips are not cultured
•  For indwelling urinary catheters, urine must be taken only from the sampling port.
• The open wound’s advancing edge of the lesion firmly sampled. 
• Pus must be expressed onto swab when incised or after it has ruptured naturally.
• If no pus, cotton swab to collect a sample from the infected site and immerse in Amies transport medium
•  Fluid from pustules, and blisters aspirated using a sterile needle and syringe.
•  Serous fluid from papules may contain treponemes: A drop of the exudate directly placed on a clean cover glass and invert it on a clean slide and examination by dark-field microscopy
• For CSF collection, patient should be fasting.
•  For CSF, lumbar puncture
•  CSF collected in two containers: one for culture and one for other purposes
•  Blood collection in two containers: for aerobic n anaerobic

Timing of Specimen Collection:

• Collection before antimicrobial therapy usage
•  Based upon the type of infectious disease process

Transport of Clinical Specimens:

•  Preferably within 2 hours
•  If delay, a suitable transport medium must be used
•  Preservation using Boric acid (urine)
•  Anticoagulants: For blood, synovial fluid, bone marrow
• Sodium Polyanethol Sulfonate (SPS), Heparin, Citrate, EDTA

Storage Guidelines for Different Specimen Types:

• Specimens that CAN be refrigerated: Urines, Respiratory Exudates, Stools/Feces, Wounds
•  Specimens that cannot be refrigerated: Spinal Fluids and Other Body Fluids, Genital/Cervical for Gonococcus Isolation, Blood

Criteria for Specimen Rejection:

• If information on label doesn’t match the information on requisition form
•  If specimen is transported at improper temperature
•  If specimen is not in appropriate media
•  If specimen quantity not sufficient
•  If specimen is received in fixative
•  If specimen is leaking
  

SPECIMEN SELECTION	POSSIBLE BACTERIA	COLLECTION EQUIPMENT	TRANSPORT
Wounds, Abscesses 1. Purulent drainage 2. Tissue affected 3. Body fluids 4. Ulcers 5. Wound margins	Staphylococcus aureus, Anaerobes (deep wounds, aspirates only), Enterobacteriaceae, Streptococcus species, Clostridium species, Enterococcus, Pseudomonas aeruginosa	Wounds (surface) Swab   Wound (deep) Syringe Anaerobic swab kit	Transport medium   Anaerobic transport Transport the aspirate in the collecting syringe or Put aspirate into anaerobic broth or Gather pus with the swab and insert it straight into anaerobic transport
Bacterial Throat-Pharynx Infections (swabs and nasopharyngeal aspirates)	Streptococcus pyogenes, Haemophilus influenza, Corynebacterium diphtheria, Neisseria meningitides, Neisseria gonorrhoeae, Bordetella pertussis, Fusobacterium species	Nasopharynx Cotton-tipped nichrome or stainless wire-28 gauge   Throat Swab (tongue blade is necessary)	Nasopharynx: Do not refrigerate Transport medium       Throat: Transport medium if more than 2 h delay to laboratory
Bacterial Pulmonary Infections 1. Transtrachael aspirate 2. Lung aspirate/biopsy 3. Sputum	Streptococcus pneumoniae, Haemophilus species, Staphylococcus, Klebsiella species, Other Enterobacteriaceae, Mycobacterium	Sterile cup	Sputum Refrigerate  if needed Transport in collection container
Specimen	Possible bacteria	Collection equipment	Transport
Possible Septicemia 1. Blood	Staphylococcus species, Escherichia coli, Klebsiella species, Pseudomonas species, Bacteroides species, Enterococcus, Streptococcus pneumoniae	Commercial kit Needle and syringe	Culture broth in bottles 50 ml/bottle.  5 ml blood/ bottle. 2 bottles; one aerobic, one anaerobic. Do not refrigerate 100 ml/bottle with 10 ml blood/bottle.
Bacterial Diarrhea Stool, Rectal swab	Salmonella species, Shigella species, Escherichia coli, Vibrio species, Staphylococcus aureus, Yersinia species, Campylobacter jejuni (special media required)	Clean or sterile collection cup Swab (only if necessary)	Refrigerate if not plated within 1 hour Swab into transport medium Carey-Blair recommended for Campylobacter sp.

Specimen	Possible bacteria	Collection equipment	Transport
Genital Tract 1. Cervix 2. Urethral discharge	Neisseria gonorrhoeae, Treponema pallidum	Swab	Do not refrigerate Immediate CO2 for GC
Urinary Tract Infections 1. Clean catch midstream      2. Suprapubic aspirate 3. Catheterization	Escherichia coli, Klebsiella species, Proteus mirabilis, Pseudomonas, Enterococcus	Urine (midstream) Sterile screw-cap cup   Urine (catheter)Sterile screw-cap tube Needle and syringe	Transport in collection container Refrigerate quickly   Sterile tube
Bacterial Meningitis Spinal fluid	Neisseria meningitides, Streptococcus pneumonia, Haemophilus influenza, Streptococcus, Enterobacteriaceae,  Staphylococcus aureus,  Streptococcus – Group B	Surgical prep and collection by physician  Sterile screw-cap or snap-cap tubes	Transport in collection tube. Do not refrigerate