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Clinician Guide for Collecting Cultures

Ed Septimus, MD, FACP, FIDSA, FSHEA 
Medical Director Infection Prevention and Epidemiology 

Source: HCA Clinical Services Group, Nashville, TN 

If possible cultures should be obtained before starting antimicrobial therapy; prior antimicrobial therapy may interfere with bacterial growth.

Blood cultures

  • Disinfect bottle tops with 70% isopropyl alcohol (alcohol pad);  clean puncture site with alcohol followed by chlorhexidine (CHG) and allow to dry
  • For adults, collect 10-20 cc and 1-3 cc for a child for each blood culture set; divide blood into two blood culture bottles, one for aerobes and one for anaerobes;  two or three blood cultures (by separate stick) per septic episode is sufficient.
    • Laboratory confirmed bloodstream infection (not central line related)
      • 1 positive blood culture with recognized pathogen from a  venipuncture
      • Skin organisms: >2 blood cultures drawn on separate occasions positive for the same organism plus clinical symptoms
  • For suspected catheter-related bloodstream infection (CR-BSI) draw one set through device and one set from a separate venipuncture.  Blood cultures from both line and venipuncture must be positive for same organism with clinical signs and symptoms and no other recognized source.  A positive culture from the line only is probably a contaminant and should not be treated.
    • Preferred Criteria for CR-BSI:
      • Differential  period of central line culture versus peripheral blood culture positivity > 2 hours
      • Simultaneous quantitative blood cultures with a ≥5:1 ratio central line versus peripheral blood culture
    • Alternative:
      • Draw one set through device and one set from a separate venipuncture for routine blood culture

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Intravenous catheter tips

  • Remove aseptically and cut a ~4 cm segment from tip and place in sterile container; transport rapidly to prevent drying out;
    • Semiquantitative culture of catheter tips is usually performed by rolling the tip across an agar plate; the presence of >15 colonies along with the same organism isolated from peripheral blood with clinical signs and symptoms and no other recognized source  is consistent with a CR-BSI.
      (Note: Determining if a BSI is a CR-BSI may be useful clinically. However, this definition of CR-BSI is not used for surveillance of CLABSI through NHSN. For the NHSN surveillance criteria, please refer to [PDF – 141.23 KB])
  • Comment: A positive catheter tip by itself is not diagnostic for a CR-BSI;   Do not routinely culture catheter tips on removal unless there are clinical signs and symptoms for infection.

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  • Clean surface of wound or abscess with 70% alcohol and allow to dry;  aspirate pus or fluid if possible and either transport in syringe(preferred) or  place in anaerobic transport vial;  anaerobic transport tubes are appropriate for aerobic and anaerobic cultures;  always request a gram stain for initial guidance and comparison
  • Swabs should be discouraged since swabs usually have insufficient material for gram stain and culture;  if swabs must be used be sure quantity is adequate for both culture and gram stain
  • Do not culture chronic superficial wounds or sinus drainage since superficial cultures correlate poorly with deep cultures-try an obtain a deep culture or biopsy for culture whenever possible

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  • Have patient rinse with water to remove excess oral flora; instruct patient to cough deeply and collect and transport in a sterile container;  microbiology should perform a cytologic screening  specimens that are contaminated with oral secretions (presence of >10 squamous epithelial cell/LPF) and recommend re-collection if specimen is inadequate; gram stain should be performed on all sputum specimens

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Tracheal aspirate

  • Does not need to be screened like sputum; perform gram stain along with routine cultures;  lab should report if specimen is purulent (>25 WBC/LPF)

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Bronchial alveolar lavage (BAL) and mini-BAL

  • Obtained by bronchosopy or with use of a special catheter(mini-BAL); requires  prompt transport to the laboratory for processing;  not acceptable for anaerobic cultures; fluid should be concentrated for optimal yield for stains and cultures; consider quantitative bacterial cultures to guide interpretation with >104 CFU/mL considered significant

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  • Midstream
    • Instruct women to hold labia apart, discard the first portion of voided urine and collect midstream urine in a sterile container
    • Instruct men to retract foreskin(uncircumcised), discard first portion of voided urine and collect in sterile container
  • Catheterized
    • Short-term collect specimen by aseptically aspirating from port of urinary catheter
    • Long-term change urinary catheter: first change urinary catheter then collect specimen by aseptically aspirating port of urinary catheter
    • Caution: straight cath for urine collection may result in iatrogenic UTI
  • Transport: keep urine refrigerated and send to microbiology lab promptly;  if significant delay is anticipated (e.g. regional lab) put urine in a tube with boric acid to prevent overgrowth  of contaminating organisms
  • Comment: Do not treat asymptomatic bacteriuria except in pregnancy or GU instrumentation

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  • Collect specimen in a sterile container and transport promptly to microbiology lab; notify micro if a specific pathogen suspected (e.g. Vibrio, Yersinia, E. coli O157:H7, C. difficle)
  • Comments:
    • In general do not process for bacterial pathogens if patient develops symptoms more than 3 days after admission; consider C. difficile for hospitalized patients with diarrhea
    • Multiple specimens per day are not indicated
    • Formed stools in general should not be submitted

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  • For bacteria send 1-2 mL for bacteria; if mycobacteria or fungi suspected send 5-10 mL
  • Comments
    • In general for initial evaluation, send CSF for cell count, glucose (also draw simultaneous blood glucose), and protein with gram stain and bacterial culture
    • Do not routinely order bacterial antigens, AFB, and fungi, or PCR for herpes until initial results from routine studies are available;  drawing  an extra tube to save for additional studies pending initial results is more appropriate and cost effective

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