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Lab Manual for UCSF Clinical Laboratories

Lab Manual for SFGH

Internal Resources

Microbiology Procedures


A. Microbiology Laboratory Hours:

Routine Hours:

Monday - Friday, 8 am - 5 pm

Emergency (STAT) Service:

24 hours, 7 days

B. Telephone Numbers:

Microbiology - Information and Results: 415-206-8576

C. Antimicrobial Susceptibility Studies (ZSFG Antibiogram)

Click on links for the current Antimicrobial Susceptibility Studies (ZSFG Antibiogram 2016) card and an accompanying memo .


Some microbiology tests are performed ONLY after consultation with a Laboratory Medicine Resident. See ALPHABETICAL LIST OF TESTS for further information. A Laboratory Medicine Resident is also available for consultation regarding microbiology problems.

  • Monday - Friday, 8 am - 5 pm, 415-206-5699, or pager number 415-443-1438

At all other times, call the Clinical Laboratory Information Section (Inquiry) at 415-206-8590, and request their assistance to contact the Lab Medicine Resident on call.

  1. Antigen detection in CSF, Urine, and other body fluids, see Antigen Detection in Body Fluids in the Alphabetical Tests

  2. Bordetella pertussis PCR

  3. CMV IgM

  4. CMV Detection in Blood or Bone Marrow (PCR)

  5. CSF-PCR tests

  6. Histoplasma Antigen, Urine

  7. Legionella Urine Antigen

  8. Lyme Disease Serology

  9. Pneumocystis Diagnosis: Use Chest Service Requisition to obtain these services. The Chest Service Fellow collects bronchoalveolar lavage or transbronchial biopsies via bronchoscopy and coordinates with the Microbiology Laboratory. Tracheal or bronchial aspirates are accepted only from patients who are intubated.

  10. Release antimicrobial susceptibility test results not routinely reported.

  11. Rotavirus Antigen

  12. Rubella Virus Isolation

  13. Serum Killing Level (SKL), Serum Cidal Test or Serum Antibacterial Titers, see Antimicrobial Serum Killing level.

  14. Syphilis - Treponema pallidum, Darkfield.

  15. Toxoplasma IgM

  16. Susceptibility: Non-routine tests – fungal, viral, AFB, tube dilution antimicrobial susceptibility tests, time kill curve, killing rate by antimicrobial, combined antimicrobial activity and synergy tests, see Antimicrobial Susceptibility.

  17. Touch Preparation (Impression Smear). This exam is useful for finding parasites (e.g., toxoplasma) and fungi in tissue. Notify Microbiology Resident when biopsies of brain, lung or other tissues are scheduled. Place biopsy on moist Telfa and transport to lab as soon as possible. Do Not Fix Tissue or Float in Saline for this exam.


  1. The requisition form must have complete information, including specimen source, or the specimen will not be processed. See instructions in the General Information Section, “Completing the Requisition Form.” In order to ensure proper selection of media and techniques, designate suspected organisms and diagnoses whenever possible. All specimens, whether in collection container or inoculated to culture media, must be labeled with the patient’s complete name, medical record number, and date and time of collection. The practice of wrapping the specimen or cultures in the requisition slip is not adequate labeling, since the requisition slip may be lost or interchanged in transport to the laboratory. All specimens must be placed in a biohazard bag; place the requisition in the outer pouch. Do not put the requisition inside the biohazard bag.

  2. Specific specimen collection instructions appear under each procedure entry.

  1. Do not send specimens such as pus, exudates, fluids, tissues, or catheter tips in Transport Medium because they become buried and lost. Do not send specimens in a syringe with needle attached. Send these specimens in a sterile, screw-top tube. Swab-collected specimens should be put into Transport Medium before sending them to the laboratory. Swab collected specimens are not satisfactory for culture of anaerobes or AFB. See instructions for special anaerobic culture below. For large volume collections, large volume, sterile, evacuated bottles are available from the Pharmacy.

    Bone marrow for bacterial, mycology or AFB culture should be drawn into a bright green top (heparin) tube.

    Bone marrow for detection of viruses by PCR must be drawn into lavender top (EDTA) tube

  2. Anaerobic Bacteria Culture Collection

    Collect specimens for anaerobic culture in carbon dioxide-filled anaerobic collection tube. Call Lab Support Services 415-206-8199 to restock these tubes.

a. Procedures for Specimen Collection


Specimens & Method of Collection


Aspirated or biopsy material

Pulmonary area

Needle aspiration of an abscess or biopsy

Abdominal area

Paracentesis fluid, or aspiration of deep abscess by needle and syringe

Female genital tract

Laparoscopy specimens, surgical specimens or aspirations by needle & syringe

Bone and joint

Aspirates of joint fluid or deep aspirates of drainages by needle & syringe.

Soft tissue

Deep aspirates, surgical specimens, biopsy material of tissue, aspirates of drainages or pus by needle and syringe

Cultures for obligate anaerobes are appropriate for wounds and abscesses in any location in the body. When infection is thought to have entered the body from any level of the gut, anaerobes should be considered as part of the infecting flora, e.g., peritonitis following penetrating wounds of the intestine, appendicitis or diverticulitis. The best specimens for determining lower respiratory tract infection, pulmonary abscess, and aspiration pneumonia are collected by needle aspiration of an abscess or biopsy.

In situations where an anaerobe is suspected (e.g., pulmonary, abdominal, or brain abscess; wounds with much necrotic tissue, or drainage with a particularly fetid odor), use a sterile syringe and needle to aspirate fluid. A small amount of sterile non-bacteriostatic saline may be injected into the wound or abscess if fluid cannot be readily aspirated. Eject bubbles from specimen. (To eject air from syringe before injecting specimen into anaerobic collection tube, invert an empty, sterile tube over the needle to catch any aerosols or specimen expressed with the air). Inject specimen into anaerobic collection tube.

Debrided tissue can also be put into the anaerobic collection tube. Hold tube upright with cap on top. Unscrew cap and septum. Do not tip tube, or carbon dioxide in tube will pour out and air will go into the tube. Put small strips of tissue into the tube. Screw cap and septum back in place.

The anaerobic collection tube is satisfactory for both anaerobic and aerobic cultures. Send entire tube full, if possible. Hold at room temperature--do not refrigerate or incubate. Swabs in transport media are not satisfactory for the isolation of anaerobes and will not be routinely processed for such (aerobic cultures only will be done). DO NOT put tissue or aspirates into transport medium. It will never be seen again. Submit these specimens in an anaerobic collection tube or in a sterile, screw-top tube or container.

Blood specimens are routinely cultured for anaerobes from the usual culture collection containers used for these specimens. For CSF, if anaerobes are suspected, an anaerobic collection tube should also be sent.

b. Specimen Selection for Anaerobic Culture




Draining wounds

Surgical specimens


Not Acceptable**



Bronchial washings

Vaginal or cervical swab

Surface swabs

Material adjacent to membrane

** These specimens may normally contain anaerobic bacteria not related to infection and are therefore unacceptable for anaerobic culture, even if received in anaerobic collection tubes.


(Submit specimen with properly filled-out requisition)

Culture for C. trachomatis, C. psittaci, or C. pneumoniae

(Call 415-824-5115 for more information)

Acceptable specimen: tissue, conjunctiva, nasopharynx, broncho-aveolar lavage, sputum, cervix, urethra, rectum, vaginal from females < 12 y/o.

Universal Viral Transport Medium *

Collection (for Culture)

Clean away mucus or discharge before collecting specimen. Collect specimen with swab packaged with the transport medium (regular or small-tipped swab). Specimens must contain columnar epithelial cells. Immerse swab or actual specimen (tissue, aspirate) in transport liquid in tube. Cap tube lightly. Do not send urines or specimens collected for molecular testing for culture. Refrigerate & deliver to lab within 72 hours of collection.

*Available from Lab Support Services, M-F 8:00 am-5:00 pm. Call 415-206-8199.


STOOL SPECIMENS (please indicate Date & Time of Collection on vial & requisition)

Para-Pak C&S
(pink fluid, orange cap)

(clear fluid, white cap)

Sterile Cup

Bacterial Stool Culture

Routine: Salmonella, Shigella, Campylobacter

By request: Vibrio, E. coli O157, Yersinia

Refrigerate and deliver to lab within 72 hours of collection.

Also acceptable for Giardia Antigen. Refrigerate and deliver to lab within 72 hours of collection.

Ova and Parasites (O&P)

Routine O&P includes Cryptosporidia, Isospora & Cyclospora

Giardia Antigen

Microsporidia Exam

Refrigerate and deliver to lab within 7 days of collection.

C. difficile Toxin

Helicobacter pylori Antigen

Viral Culture

Refrigerate and deliver to lab within 24 hours of collection.


For all tests on stool specimens, with the exception of Giardia Antigen, only one (1) specimen per 24 hour time period will be accepted and tested. For Giardia Antigen, only one (1) specimen per 7 day time period will be accepted and tested.

For Collection Kits, call Laboratory Support Services M-F 8:00 am-5:00 pm, 415-206-8199.


The Microbiology Division, 415-206-8576, may be contacted about the handling of emergency specimens and plating, and for information about tests in progress. Although the Microbiology Laboratory is open 24 hours daily, service in Serology, Mycology, Parasitology, and AFB is not provided after 5 pm on weekdays or at any time on weekends or holidays, except upon approval by the Microbiology Division. Sunday Bacteriology service is limited to set up of all new cultures and work-up of blood, CSF or known emergency cultures. No other cultures are examined on Sundays and reports on their progress cannot be given.


Every effort should be made to obtain all cultures just prior to the routine laboratory messenger pick-ups, so that the specimen can arrive promptly in the laboratory for proper culturing. Specimens obtained after regularly scheduled pick-ups must be sent by special messenger or brought to the Microbiology Laboratory by the physician or other ward personnel.


Miller JM. 1999. A Guide to Specimen Management in Clinical Microbiology, 2nd ed. ASM Press, Washington, DC.

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