Major Changes to Microbiology Ordering and Testing with Epic Beaker

Effective Saturday, August 2, 2014, the Epic Beaker laboratory information system will be implemented for Microbiology testing and ordering.  Several major changes to ordering and testing are summarized below, ordered by likely impact to clinical practice.

  1. All Microbiology orders will convert from generic to direct orders, summarized in the table below.  Blood culture orders will remain the same.  Preference lists and SmartGroup order sets have been updated to reflect this change.  For problems with ordering or SmartGroups please contact the Helpdesk (6-0001).

    2. Current Orderable

    Beaker Orderable

    Microbiology: Genital Tract [LAB5839]

    Aerobic culture [LAB4801]
    Yeast culture [LAB241]
    Group B Strep culture [LAB7471]
    CNPCR [LAB2223]
    NGPCR [LAB2372]
    Wetprep for trichomonas, gardnerella, candida [LAB7263]
    Gram stain for Bacterial vaginosis [LAB2336]

    Microbiology: Respiratory [LAB5840]

    Respiratory culture [LAB2397]
    Fungal culture [LAB240]
    AFB culture [LAB2208]
    Quantitative culture [LAB2392]
    Grp A Strep culture [LAB7975]
    Respiratory virus Panel PCR [LAB7366]
    Influenzae A/B  PCR [LAB7455]
    MRSA PCR [LAB5810]
    Pneumocystis DFA [LAB2384]

    Microbiology: Sterile Body Fluid [LAB541]

    Aerobic culture [LAB4801]
    Anaerobic culture [LAB2210]
    Fungal culture [LAB240]
    AFB culture [LAB2208]
    Cryptococcal Antigen [LAB2233]
    Sterile Body Fluid, Automated [LAB2413]

    Microbiology: Stool GI Aspirate [LAB5842]

    Stool culture (includes E. coli Shiga Toxin by EIA) [LAB223]
    E. coli Shiga Toxin by EIA [LAB5717]
    C. difficile PCR [LAB4899]
    Rotavirus antigen [LAB264]
    Giardia/Cryptosporidium Assay [LAB2232]

    Microbiology: Tissue Wound [LAB5843]

    Aerobic culture [LAB4801]
    Anaerobic culture [LAB2210]
    Fungal culture [LAB240]
    AFB culture [LAB2208]
    Quantitative culture [LAB2392]

    Microbiology: Urine [LAB5844]

    Urine Culture [LAB239]
    Fungal culture [LAB240]
    AFB Culture [LAB2208]
    Yeast Culture [LAB241]

  2. Add-on cultures for urine samples sent for urinalysis will no longer be accepted.  Please send separate samples for urinalysis and culture.
  3. Cryptococcal antigen testing will convert to a new method (IMMY lateral flow).  Titers have been calibrated to the prior method (Meridian CALAS latex agglutination).  Please see the Pathology Handbook for further discussion.
  4. Standard sputum and tracheal aspirate rejection criteria will be applied to all patients except cystic fibrosis and NICU patients.  Rejection criteria do not apply to lower respiratory samples and are based only on the number of epithelial cells from the mouth present.  This change will affect rare pediatric patients only; in unusual circumstances rejected samples can be reconsidered for culture by paging the Microbiology resident on call at 4903.
  5. Culture of intravascular catheter tips has not been performed for years and is therefore no longer orderable.  Consultation with the pathology resident on call (pager 4903) should be made regarding order entry and specimen handling of unusual or nonstandard specimens for culture.

Questions concerning testing can be directed to Bradley Ford, MD, PhD, Medical Director of Microbiology (ext. 6-2990, pager 8290).